To tell if they're hacked, do the following:
Check where the pokemon was caught- if they where caught in a spot they can't be found, they're definitely hacked.
See what level it was caught on- if its a way higher level than it can be caught it was hacked.
Edit: I only clone in emerald also, because I went through the trouble of getting the pokemon and i want one in my emerald and one in diamond. Its not hacking. Someone just found a glitch in the game. I want to go back and play my emerald and have a pokemon i loved and be able to use it in pokemon diamond. Emerald cloning glitch Is as criminal as the glitch in japanese pokemon diamond where you can get arceus and shaymin without hacking.