Atmosphere likely won't be touched by Nintendo because it doesn't support backup loading. Sure does Nintendo not want any unlicensed software running on their consoles yes, but in many countries homebrew itself is legal and where the authors and contributors of AMS refuse to enable backup loading they should be fairly safe from Nintendo's wrath.
I just don't see it worth Nintendo's time, money and resources to pursue AMS legally as it would for one, likely be fruitless and two wouldn't have an effect on piracy anyways as AMS doesn't support it out of the box. I mean it does support emulation but I digress.
We all know emulation is legal pretty much everywhere and its up to the end user to violate copyright laws or not with pirated roms or legally using their own game dumps.