I don't know, do I look like I work for Nintendo?
In all seriousness, it wouldn't be far-fetched for Nintendo to conduct a simple hash check for any save files uploaded to their cloud. But this is Nintendo we're talking about so they may not conduct that check when save data is uploaded; they may only conduct checks when it is being actively used on a game or if there are other traces of save data modification such as with an illicit error code.