ADDITIONAL SYSTEM INFORMATION :
Java:
  openjdk version "11.0.2" 2019-01-15
  OpenJDK Runtime Environment 18.9 (build 11.0.2+9)
  OpenJDK 64-Bit Server VM 18.9 (build 11.0.2+9, mixed mode)

Operating System:
  Windows 10 Enterprise
  Version: 1909
  Installed on : 01/06/2021
  OS Build: 18363.1916
  
Maven -version details:
  Apache Maven 3.8.4 (9b656c72d54e5bacbed989b64718c159fe39b537)
  Maven home: C:\BuildTools\apache-maven-3.8.4
  Java version: 11.0.2, vendor: Oracle Corporation, runtime: C:\BuildTools\jdk-11.0.2
  Default locale: en_GB, platform encoding: Cp1252
  OS name: "windows 10", version: "10.0", arch: "amd64", family: "windows"


A DESCRIPTION OF THE PROBLEM :
When building a simple example which also uses the maven-assembly-plugin
assembly warnings are output:

[INFO] [INFO] --- maven-assembly-plugin:3.3.0:single (default) @ hellofx ---
[INFO] Reading assembly descriptor: src/main/assembly/zip.xml
[WARNING] Failed to build parent project for org.openjfx:javafx-controls:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-controls:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-graphics:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-graphics:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-base:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-base:jar:17.0.1

JavaFX Releases 11 to 16 do not output the warning messages.

REGRESSION : Last worked in version 16.0.2

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
A maven project is created with the following directory structure
    openjfx-assembly-warnings\data\someData.txt
openjfx-assembly-warnings\scripts\run.bat
openjfx-assembly-warnings\src\main\assembly\zip.xml
openjfx-assembly-warnings\src\main\java\HelloFX.java
openjfx-assembly-warnings\pom.xml

The file contents are:

someData.txt
  This file represents some data
  to be zipped up along with the
  application jar file

run.bat
  java -cp ".;lib\*" HelloFX
  
zip.xml
  <assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
            xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
            xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
http://maven.apache.org/xsd/assembly-1.1.2.xsd">
    <id>zip</id>
    <includeBaseDirectory>true</includeBaseDirectory>
    <formats>
      <format>zip</format>
    </formats>
    <fileSets>
      <fileSet>
        <directory>${project.basedir}/scripts</directory>
<outputDirectory>/</outputDirectory>
      </fileSet>
<fileSet>
        <directory>${project.basedir}/data</directory>
<includes>
<include>*</include>
        </includes>
<outputDirectory>/data</outputDirectory>
      </fileSet>
    </fileSets>
    <dependencySets>
      <dependencySet>
        <outputDirectory>/lib</outputDirectory>
      </dependencySet>
    </dependencySets>
  </assembly>

HelloFX.java
  import javafx.application.Application;
  import javafx.scene.Scene;
  import javafx.scene.control.Label;
  import javafx.scene.layout.StackPane;
  import javafx.stage.Stage;

  public class HelloFX extends Application {

    @Override
    public void start(Stage stage) {
      String javaVersion = System.getProperty("java.version");
      String javafxVersion = System.getProperty("javafx.version");
      Label l = new Label("Hello, JavaFX " + javafxVersion + ", running on Java " + javaVersion + ".");
      Scene scene = new Scene(new StackPane(l), 640, 480);
      stage.setScene(scene);
      stage.show();
    }

    public static void main(String[] args) {
      launch();
    }
  }

pom.xml
  <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <name>hellofx</name>
    <groupId>com.test</groupId>
    <artifactId>hellofx</artifactId>
    <version>1.0.1</version>
    <packaging>jar</packaging>
    <url>http://maven.apache.org&lt;/url>
    <properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>
    <dependencies>
      <dependency>
        <groupId>org.openjfx</groupId>
        <artifactId>javafx-controls</artifactId>
        <version>17.0.1</version>
      </dependency>
    </dependencies>
    <build>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.8.1</version>
          <configuration>
            <release>11</release>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>exec-maven-plugin</artifactId>
          <version>3.0.0</version>
          <executions>
            <execution>
              <goals>
                <goal>java</goal>
              </goals>
            </execution>
          </executions>
          <configuration>
            <mainClass>HelloFX</mainClass>
          </configuration>
        </plugin>
   <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>3.3.0</version>
          <executions>
            <execution>
              <phase>package</phase>
              <goals>
                <goal>single</goal>
              </goals>
              <configuration>
                <appendAssemblyId>false</appendAssemblyId>
                <descriptors>
                  <descriptor>src/main/assembly/zip.xml</descriptor>
                </descriptors>
              </configuration>
            </execution>
          </executions>
        </plugin>
      </plugins>
    </build>
  </project>

To reporduce, run the maven command : mvn clean install

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
----Expected Result----
The expected result should be maven build output as follows:
[INFO] Scanning for projects...
[INFO]
[INFO] --------------------------< com.test:hellofx >--------------------------
[INFO] Building hellofx 1.0.1
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ hellofx ---
[INFO] Deleting C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ hellofx ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\src\main\resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hellofx ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\classes
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ hellofx ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\src\test\resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ hellofx ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ hellofx ---
[INFO] No tests to run.
[INFO]
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ hellofx ---
[INFO] Building jar: C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.jar
[INFO]
[INFO] --- maven-assembly-plugin:3.3.0:single (default) @ hellofx ---
[INFO] Reading assembly descriptor: src/main/assembly/zip.xml
[INFO] Building zip: C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.zip
[INFO]
[INFO] --- maven-install-plugin:2.4:install (default-install) @ hellofx ---
[INFO] Installing C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.jar to C:\Users\T0082584\.m2\repository\com\test\hellofx\1.0.1\hellofx-1.0.1.jar
[INFO] Installing C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\pom.xml to C:\Users\T0082584\.m2\repository\com\test\hellofx\1.0.1\hellofx-1.0.1.pom
[INFO] Installing C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.zip to C:\Users\T0082584\.m2\repository\com\test\hellofx\1.0.1\hellofx-1.0.1.zip
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.867 s
[INFO] Finished at: 2021-12-23T10:03:24Z
[INFO] ------------------------------------------------------------------------

As can be seen no WARNING messages are output.


ACTUAL -
The actual result is producing WARNING messages with output as follows:

[INFO] Scanning for projects...
[INFO]
[INFO] --------------------------< com.test:hellofx >--------------------------
[INFO] Building hellofx 1.0.1
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ hellofx ---
[INFO] Deleting C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ hellofx ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\src\main\resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hellofx ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\classes
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ hellofx ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\src\test\resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ hellofx ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ hellofx ---
[INFO] No tests to run.
[INFO]
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ hellofx ---
[INFO] Building jar: C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.jar
[INFO]
[INFO] --- maven-assembly-plugin:3.3.0:single (default) @ hellofx ---
[INFO] Reading assembly descriptor: src/main/assembly/zip.xml
[WARNING] Failed to build parent project for org.openjfx:javafx-controls:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-controls:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-graphics:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-graphics:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-base:jar:17.0.1
[WARNING] Failed to build parent project for org.openjfx:javafx-base:jar:17.0.1
[INFO] Building zip: C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.zip
[INFO]
[INFO] --- maven-install-plugin:2.4:install (default-install) @ hellofx ---
[INFO] Installing C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.jar to C:\Users\T0082584\.m2\repository\com\test\hellofx\1.0.1\hellofx-1.0.1.jar
[INFO] Installing C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\pom.xml to C:\Users\T0082584\.m2\repository\com\test\hellofx\1.0.1\hellofx-1.0.1.pom
[INFO] Installing C:\Users\T0082584\Desktop\Work\OPUS-G_Repositories\openjfx-archive-warnings\target\hellofx-1.0.1.zip to C:\Users\T0082584\.m2\repository\com\test\hellofx\1.0.1\hellofx-1.0.1.zip
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.851 s
[INFO] Finished at: 2021-12-23T10:05:00Z
[INFO] ------------------------------------------------------------------------

---------- BEGIN SOURCE ----------
A maven project is created with the following directory structure
    openjfx-assembly-warnings\data\someData.txt
openjfx-assembly-warnings\scripts\run.bat
openjfx-assembly-warnings\src\main\assembly\zip.xml
openjfx-assembly-warnings\src\main\java\HelloFX.java
openjfx-assembly-warnings\pom.xml

The file contents are:

someData.txt
  This file represents some data
  to be zipped up along with the
  application jar file

run.bat
  java -cp ".;lib\*" HelloFX
  
zip.xml
  <assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
            xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
            xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
http://maven.apache.org/xsd/assembly-1.1.2.xsd">
    <id>zip</id>
    <includeBaseDirectory>true</includeBaseDirectory>
    <formats>
      <format>zip</format>
    </formats>
    <fileSets>
      <fileSet>
        <directory>${project.basedir}/scripts</directory>
<outputDirectory>/</outputDirectory>
      </fileSet>
<fileSet>
        <directory>${project.basedir}/data</directory>
<includes>
<include>*</include>
        </includes>
<outputDirectory>/data</outputDirectory>
      </fileSet>
    </fileSets>
    <dependencySets>
      <dependencySet>
        <outputDirectory>/lib</outputDirectory>
      </dependencySet>
    </dependencySets>
  </assembly>

HelloFX.java
  import javafx.application.Application;
  import javafx.scene.Scene;
  import javafx.scene.control.Label;
  import javafx.scene.layout.StackPane;
  import javafx.stage.Stage;

  public class HelloFX extends Application {

    @Override
    public void start(Stage stage) {
      String javaVersion = System.getProperty("java.version");
      String javafxVersion = System.getProperty("javafx.version");
      Label l = new Label("Hello, JavaFX " + javafxVersion + ", running on Java " + javaVersion + ".");
      Scene scene = new Scene(new StackPane(l), 640, 480);
      stage.setScene(scene);
      stage.show();
    }

    public static void main(String[] args) {
      launch();
    }
  }

pom.xml
  <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <name>hellofx</name>
    <groupId>com.test</groupId>
    <artifactId>hellofx</artifactId>
    <version>1.0.1</version>
    <packaging>jar</packaging>
    <url>http://maven.apache.org&lt;/url>
    <properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>
    <dependencies>
      <dependency>
        <groupId>org.openjfx</groupId>
        <artifactId>javafx-controls</artifactId>
        <version>17.0.1</version>
      </dependency>
    </dependencies>
    <build>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.8.1</version>
          <configuration>
            <release>11</release>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>exec-maven-plugin</artifactId>
          <version>3.0.0</version>
          <executions>
            <execution>
              <goals>
                <goal>java</goal>
              </goals>
            </execution>
          </executions>
          <configuration>
            <mainClass>HelloFX</mainClass>
          </configuration>
        </plugin>
   <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>3.3.0</version>
          <executions>
            <execution>
              <phase>package</phase>
              <goals>
                <goal>single</goal>
              </goals>
              <configuration>
                <appendAssemblyId>false</appendAssemblyId>
                <descriptors>
                  <descriptor>src/main/assembly/zip.xml</descriptor>
                </descriptors>
              </configuration>
            </execution>
          </executions>
        </plugin>
      </plugins>
    </build>
  </project>

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
The only work around is to use a version of JavaFX prior to version 17