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Based on my reading of the Mac App Store approval guidelines, I don't see how Java or Flash (in their current forms) could possibly be distributed via the App Store. The terms explicitly forbid apps from installing any shared frameworks, or modifying existing apps in any way.

I also assume that every Mac is going to have to be assigned a UDID now, unless Apple is completely reinventing their DRM scheme. Regardless, the piracy options for Mac apps are almost certainly going to be similar to their iOS cousins, if not a little easier because every Mac is effectively "rooted" out of the box.

If Adobe provides a tool to convert Flash into a Cocoa app, akin to their tool for producing iPhone apps, those would presumably be allowed in the App Store.

On Java, no speculation required:

2.24 Apps that use deprecated or optionally installed technologies (e.g., Java, Rosetta) will be rejected.