(This is simply a spec consistency issue.)
Component.hide() and Component.show() are marked as deprecated, but Window.hide() and Window.show() are not. This appears to merely be the result of an oversight when these methods were overridden. Since they are not deprecated, it gives the impression that these methods do something different than what Window.setVisible(true/false) would do, which is not the case.
Although this is not a critical issue, I regularly receive inquiries about it from external spec reviewers, so it is causing some bit of confusion. It would be helpful if these methods were simply marked as "deprecated" for the sake of consistency.