You should be safe. There were banwaves in the past that resulted in players getting blocked from online play, but those were tied to the console, not the account, and there is no 3DS online play to ban people from anymore. And after those banwaves happened, CFW started getting smarter about covering its tracks so Nintendo likely can't detect you as long as everything's up to date.

Given that the 3DS has been long discontinued, Nintendo's not going to bother cracking down on anyone now.