They've all but moved on to the Switch now, the only ways you might get banned on 3DS nowadays is if you cheat online, or possibly also if you tried downloading games from the eshop using fake tickets. If you just install games and play online without cheating it shouldn't be a worry.
If you're especially worried, the gen 6 games + sun/moon all have legit cias that can run without cfw, so you could install those onto an unmodded console and use that for pokémon bank instead (would require temporarily booting into cfw to install the games though.)
In theory it would be trivial for Nintendo to notice something's off because you're not supposed to have so many preinstalled games at once on a system like this, but they don't really check for that kind of thing and they're more worried about the Switch nowadays.