The Pokémon Company International announced on their Japanese website that 5954 players have been banned so far for illegally altering save game data. Players that have been banned are unable to use any of the Pokémon Global Link's online features including: Game Sync, Rating Battles, Battle Competitions and Global Missions.

Players that have been banned will receive the Error Code: 090-0212 and a message stating that connecting to the Pokémon Global Link is prohibited.

The press release also states that they will continue to ban more player in the future without notice that illegally modify game data.

Source: https://3ds.pokemon-gl.com/information/b87bc53f-7144-44ba-9a29-59bd00330d84