With things like Pokésav and Action Replay around I can't help but wonder how Nintendo checks for legal Pokémon at their official tournaments? Legal as in, it can be generated naturally from the game, where as hacked Pokémon can't be. Are they really stern about checking everyone's Pokémon or is it only when there is reasonable supicion? Also even if you have a legal Pokémon that passes all the legality checks, if it has max IVs or are pretty darn close to max IVs, do they exercise common sense and assume the Pokémon is hacked and disqualify you? Is there some kind of forensic data finger print they can use to tell when a Pokémon was generated or altered from an external device even if it's legal? Or maybe logs in the game that could expose altering like the journal?
The exact process is unknown.
You are best off not hacking at all for any kind of tournaments, especially official ones.
Using hacked Pokemon is pretty despicable, in any case.