After signing jar I'm starting -deploy task with or without -embedCertificates option and I get the same result.
So, this option has no effect. You can look at this in the attached project:
To generate signed jar you're to invoke this:
ant -f simple-build.xml sign-jar

Then, to invoke -deploy without embedCertificates you're to invoke this:
javafxpackager -deploy -v -width 800 -height 600 -outdir dist -outfile HelloWorld -name HelloWorld -appclass helloworld.HelloWorld -srcfiles dist/HelloWorld.jar -title HelloWorld -vendor Name_Surname

With:
javafxpackager -deploy -v -width 800 -height 600 -outdir dist -outfile HelloWorld -name HelloWorld -appclass helloworld.HelloWorld -srcfiles dist/HelloWorld.jar -title HelloWorld -vendor Name_Surname -embedCertificates