For now the only way I think you can get banned seems to be:
1. Playing a game before its release online (not possible with freeshop games, only popular franchises from nintendo are checked for this most of the time)
2. Using homebrew software while having spotpass or show current game to friends enabled (Not available in freeshop)
3. Using cheats in online games / cheating pokémons but I think it is only a ban for a few weeks (no console ban, could be applied to freeshop games, be careful)
They check for not legally purchased DLC, but only disable it if it is detected as far as I know.
Games that weren't bought weren't the cause of bans as far as I know (Besides case 1 of course).