The reason why it looks like a native app, is because it's using the cocoa classes for the interface. For all intents, it is a native app. Except for the fact that the JVM still needs to run.
To check this, start the app, and then from the command line, do a ps -ax... if you see a java instance, than the JVM is running. If you don't, then either a) it is running... just inside the app's process. or b) it's not running because Project Builder compiled the java to native code -- highly unlikely.
The biggest thing going for the existance of the JVM is the fact that you can call standard java classes from within your code -- classes that are only available as java bytecode.
BTW, I think that java is an interesting way of programming for OS X. It's kind of puzzling at first, when you realise that one of the big benefits of java programming -- the platform independence -- is removed when you tie yourself to Cocoa. But, as a language, java has a lot of features that make it more desireable than C++ or obj-c. I'm thinking of writing a small app in Java w/the cocoa api, just to test the waters. But, with all the hassle of learning cocoa, I might as well jump in full tilt with a obj-c app instead... decisions, decisions...
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dennis