I'm aware that emulators aren't allowed, but there was a recent project discussed on this site about a developer who was going to try to get an Amiga emulator on the App Store. I think if it only plays specific games (like the C64 emulator on the App Store) then Apple will allow it, since they can test it and predict what will happen when users run it - unlike a totally open emulator.
Well from quick read I understood they will be selling standalone "applications" that include the emulation and the specific game, not full emulator.
Ok, so perhaps the emulator would be bundled with games which don't need KS.
Or they hack the trackloader to work without KS rom (many games already work out of the box with the KS ROM replacement included with UAE, but even if they don't it's usually trivial to hack the trackloader to work).