macOS Carbon Applications Mac App Store?

It will be allowed, but probably not much longer. Once they get all their own crap (iTunes/Quicken/some low level stuff) out of Carbon, I imagine it will go the way of the dinosaur.

Provided you don't use any deprecated APIs you shouldn't have a problem.

As for my personal opinion visa vis Carbon, I don't think Apple will deprecate it all together but they will probably deprecate APIs(meaning you cannot use them in the App store) to the point that most programmers will just get the hint and switch to Cocoa.