I once used an action replay on my pokemon pearl game, I used it to get all kanto-sinnoh pokemon and many other use full things. It, however totally messed up my pearl, I put in this egg code and I can't breed pokemon! Morel of this story is, yes it can totally mess up your game (and you can't use hacked pokemon in wi-fi things, such as Pokemon battle revolution, and pokemon events such as nationals and worlds).
I hoped this helped in some way. ;)