This has yet to be confirmed (RUMOR):

So if you are one of those people who play Pokemon Pearl or Diamond, like to use AR, and play on Wi-Fi you better watch out. Rumor has it that Nintendo will be tracking down players that decide to use codes on Pokemon. Nintendo has been able to find - catch all pokemon, national dex, and all shiny. It also appears that if you trade Pokemon with someone who has used one of these codes, you TOO will be banned from playing Pokemon on WFC. So even if you don't use the Action Replay, you might want to be cautious trading with someone over the GTS. I know that I'm not going to try this out, maybe one of you who's already beaten the game care to try?

Ouch. This is just wonderful. If the code can be altered, we shouldn't be banned. (Not that I play online with Nintendo games, but still.)

They should do what they did with Mario Kart DS and Metroid Prime Hunters, place hackers with the very high-ranked players or something. Pokemon is pretty much about knowledge of types, so why ban anyone who hacks? Those who hacked the game, most likely, don't know much about the strengths and weaknesses about Pokemon types.

Even if you are in an even match up with a hacker, your chances of winning are perfectly fine if you know how to play.