According to official VGC rules on Nuggetbridge:

An illegally manipulated pokemon is:

The use of external devices, such as a mobile app, to modify or create items or Pokémon in a player’s party is expressly forbidden. Players found to have Pokémon or items that have been tampered with will be disqualified from competition, regardless of whether the Pokémon or items belong to that player or were traded for.

So with that in mind:

Cloned from hacked pokemon = hacked
Cloned from legitimate pokemon = legitimate

This is because there is no way in telling that a cloned pokemon is indeed a clone. Not to mention the actual cloning takes place within the game cartridge itself, so it's more of a glitch rather than using an ActionReplay to create a pokemon out of thin air with illegal movesets or EV/IVs.

EDIT: Apparently if your pokemon in oras/xy have a blue pentagon, it means it's legit. It is part of the VGC's Pentagon Rule