In the long run, hackers could just make all the pokemon with legit stats, cover their tracks and no one, not even Nintendo will be able to tell the difference. With hackers flooding the GTS with "legit" hacked pokemon, just expect WiFi battles and tournaments to look a lot like NetBattle. It's not so bad when you think about it. Hardcore RPG players can still have fun breeding and beating the game over and over and the hardcore competitive crowd won't have to invest hundreds of hours to develop a great team.
As long as the stats don't exceed the theoretical maximum, I don't see any reason to worry about it. Chances are if kids are JUST hacking, they won't know how to use their pokemon properly to win battles anyways.