What version of Atmosphere are you using? I'm running the latest version of Arcropolis and Skyline with Atmosphere1.6.2, tried loading a few Smash mods but when trying to open the game it immediately closes it, trying to open it again gives me an error saying it's corrupted, when prompted to check it says the files are ok, but trying again to open the game causes the same behavior. I tried several different mods just to make sure it wasn't an issue with a specific mod not working, but they all crash the game before it loads. Opening the game without any files in the mods folder does work, but when opening the Store (which should now be the mods section) the game crashes.
My guess is that the most recent versions of Atmosphere do not support Arcropolis or Skyline, since I tried the troubleshooting section in Gamebanana and still no luck.