FWIW I've been online on Atmosphere for nearly a full year now, using mods (not to cheat; that WILL get you banned), using sys-clock, using retroarch, etc. and I haven't been banned. Been using the eShop and playing Smash online daily.
Obviously I can't promise anything, and every day when I turn on my Switch I'm prepared to see that I've been banned, but after being fine for so long I really think it's probably safe. Just don't install .nsps, don't cheat in online games like Splatoon, and don't change your Switch account's profile pic to something custom.