I suspect the revolution will either be a delving into cloud services and integrating this into OS X, *or* building an iOS layer into OS X, so OS X users can run both kinds of apps. Remember that iOS also shares the Darwin foundation with OS X, so it certainly doesn't sound impossible. And imagine being able to simply add iOS apps as e.g. gadgets in the OS X Dashboard, or install them as regular app bundles.
So to summarize, I don't think there's a compatibility problem in either case. Even if Apple switches to AMD (something that has been rumored), it wouldn't hurt compatibility since both the processor lines from Intel and AMD use the same instruction sets for 64-bit, and it would certainly not be the same grim fate as happened with the switch from PowerPC to Intel.
Edit: Exactly, I agree with CaoCao -- I think that could happen though.