Deprecation basically means that neither package will be delivered as part of the installation DVDs, and updates will not come via the Apple update mechanisms. It doesn't mean they won't be available anymore, it just means you'll have to download them directly from Oracle and Adobe.
Firstly, there’s nothing to suggest that Java won’t come from Apple but not be part of the standard OS X package.
Secondly, just because something isn’t on the OS X install DVD doesn’t mean it’s not updated via Software Update. Aperture for example is a separately purchased product but updates come through Apple Software Update automatically. On Lion, software update is likely to open up further since it’s the obvious conduit to deliver updates for apps on the Mac App Store.
Of course, if the JVM winds up coming from Oracle, I wouldn’t hold your breath for updates via Software Update.