I mean factory resets don't prevent bans in fact, people have already been banned after performing a factory reset. That being said, manually removing files from even supposed clean backups could wind up doing more harm than good. At the end of the day though, its Nintendo who decides who to ban, not us.
That's true, I guess it's impossible to say what they look at.
In any case like I said "cleaning" the USER partition just removed the garbage data,
the file and directory structure remained the same, assuming HacDiskMount didn't
add any extra data that shouldn't be there in the first place