Splatoon 2 anti-cheat measures have been secretly active in the game since version 3.1.0, which arrived back in June. The specifics of the anti-cheating measures have not been unveiled, but having edits on your data for Splatoon 2 is enough for Nintendo to flag you even if you don’t use the mods online. Apparently, players are banned one day after they are flagged.
OatmealDome is the source of this big reveal, and it’s noted there that the information has been independently verified by “Khangaroo” from Splatoon Modding Hub. It is also found that some modding activities still remain safe from being flagged by Nintendo–but that might not stay the case in the future.
When it comes to Nintendo, it’s always best to tread lightly with mods.