Action Replay is definitely not banned on Smogon, in fact, there are people on Smogon who put in their sigs alongside friend codes "May use legal hacks." If you're trying to trade off those hacks as legitimate Pokemon to other people, you will get in trouble, but the site has nothing against Pokemon hacked for battle purposes.
Edit: And at the above, yeah, I stopped following the metagame heavily after they banned Exca and Thundurus, which I felt was way excessive.