Example program:
package prv.rli.codetest;

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuBar;
import javafx.scene.control.MenuItem;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class MenuNavigationWithHiddenMenuItem extends Application {

    public MenuNavigationWithHiddenMenuItem() {
    }

    @Override
    public void start(Stage stage) throws Exception {
        stage.setTitle("Menu navigation with hidden item");
        Scene scene = new Scene(new VBox(), 400, 350);
 
        MenuBar menuBar = new MenuBar();
        Menu menuFile = new Menu("File");
        menuBar.getMenus().addAll(menuFile);
        menuFile.getItems().addAll(new MenuItem("New"), new MenuItem("Hidden"), new MenuItem("Quit"));
        menuFile.getItems().get(1).setVisible(false);
 
        ((VBox) scene.getRoot()).getChildren().addAll(menuBar);
 
        stage.setScene(scene);
        stage.show();
    }
    
    public static void main(String[] args) {
        launch(args);
    }
}

If you start the program, open the File menu and use the <Down>-Key to traverse through the menu items, the focus will cycle like this (with each press of the <Down>-Key):
* New
* New
* Quit
instea of just:
* New
* Quit
Interestingly, if you use <Tab>, things work as expected.