As reported by Oatmeal Dome, it appears that Nintendo has actually introduced an anti-cheat system to Splatoon 2 from a few months ago. Oatmeal Dome claims to have known about it for a few months now but has kept quiet as Nintendo was not actively banning users via the system, at least until another researcher has discovered it as well.
Basically the anti-cheat system will flag users who are discovered to be running model edits, replaced music in the game, text mods, and also save edits, just to name a few. Gamers who are detected doing such things will be flagged, and that players are typically banned after a day that they have been flagged (presumably they will be reviewed first to see if the detection was accurate).
This isn’t the first time we’ve seen Nintendo ban players for modding, where a few months ago it was reported that Nintendo was banning players who had modified their consoles, and also banning game cards that might have been obtained illegally.