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.
If cross-platform support is not a requirement, desktop Java is not even in the running.
https://jaxenter.com/20-javafx-real-world-applications-12365...
I don't think you will find any "great" one there, though, but some look well designed.
Other than that, it is up to a product team to actually have designers helping defining the final L&F.
[0] https://github.com/HanSolo [1] https://www.youtube.com/channel/UCCPbe_sGZuimJUyd2rdR7kA