These apps have had a lot of time put into their design–it's not just "we slapped Cocoa on this and now it's beautiful". Native apps being better is selection bias, since people who spend time on design aren't going to settle for Java messing up the UI or UX–so they just all use AppKit.
That's not exactly true or those people won't settle for Electron either. Obviously that's not the case and I wonder why. Is it just that Electron apps are easier to do, native apps look and feel better, so JavaFX is a sort of no man's land?
The point of Java on the desktop was cross-platform compatibility, but electron now occupies that same space — and decent JS developers are cheaper and easier to find than decent Java-desktop developers.
If cross-platform support is not a requirement, desktop Java is not even in the running.
These apps have had a lot of time put into their design–it's not just "we slapped Cocoa on this and now it's beautiful". Native apps being better is selection bias, since people who spend time on design aren't going to settle for Java messing up the UI or UX–so they just all use AppKit.