No, the deprecation warning is logged by getDestinationDir, but the problem is the one calling that method.
In your case it is the Java Modularity plugin.
I would anyway recommend to not use it, but to use the built-in JPMS support.
If you don’t apply the plugin manually, you should update the JavaFX plugin, as from 0.1.0 on it does not auto-apply the Java Modularity plugin anymore.