I mean, people can get away with just atmosphere since apparently Nintendo can't look at the contents of the SD card but maybe a future version of the firmware can flag atmosphere/CFW being used.
The usual ways to be banned are:
1. Cheating
2. Modding saves for some games
3. Using the file override function to play other games (The original piracy method done by impatient people)
4. Installing pirated games
You can use Atmosphere online usually. I've done it on an emunand (Atmosphere support is iffy for it on some legit games in my experience) and nand