Apple doesn't allow generic emulators for iPhone anyway, so this is a moot point. Such emulators are only possible via jailbreaking.
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.
Floppy bootable trackloading games are easy to hack to work without full KS ROM.
Ok, so perhaps the emulator would be bundled with games which don't need KS.