Multiple reasons!
Think of all the forum posts you see along the lines of 'hai guyz i dont no how 2 wurk dis emulator pleez halp me downlod roms k thx'. No official company is going to take that kind of workload on board for their technical support.
Emulators are always going to be imperfect, and no official company is ever going to publically admit to releasing an imperfect product that would give angry customers a license to threaten them over it. Sure, not many people would do that, but if there's ever the tiniest chance anything bad could happen to any end user and the company would have to admit actual responsibility in any way, shape, or form they're simply not going to do it.
Plus there aren't that many people who really want emulators. You and your mates are not lots of people. Even the entire population of this forum is not 'lots of people'. I'm pretty confident most smartphone gamers couldn't care less: they're too busy playing Angry Birds to play some dumb SNES cartridge that came out fifteen years ago.
And of course there's always money. These companies are businesses, and they have a responsibility to their shareholders to make the company worth lots of money and make the shareholders rich, otherwise the shareholders can threaten them with all kinds of things. Releasing an emulator users can do whatever they want with, or can hack to do whatever they want with, is not going to make shareholders rich. Releasing an emulator that works with one game at a time and charging lots of money for that is going to make shareholders a lot happier, because enough people still want it even if it's over-priced it'll still shift copies.
Probably more reasons, but it's really late and I can't sleep, which is the only reason I'm typing this in the first place.
