Still got a few pages left to read so apologies if someone already floated the idea.
While I probably would bet on it being some kind of basic "not legal" slip up somewhere in there, possibly even including play time, I do have to wonder if something more fun is at play; it is certainly how I would approach things. Typical save editing and cheat making is an exclusionary affair (I doubt anybody did a full disassembly/step through to make the cheat as much as compared various dumps while changing nothing/little but the value the cheat was wanted for) and you can slip things by there*, similarly if we are considering online then some kind of twist on metrics could be a thing if something is sent along to the server. That is also ignoring the option for there being some kind of tell in RAM.
*all the classic mirrored, inverted, pointer/round robin annoyances come back into play, you just have the normal game load up as the cheat would have it but secretly an alarm is going/a flag is tripped. Do it randomly or even set number of saves (people save ever few minutes and I don't know about any autosaves here) and the basic compare and find cheat method will dismiss it.
Anyway general policy for these sorts of things has always been "you hack, online is gone for you then and while you can possibly get it back that is all you", I thought it was all fairly well known but I guess if Nintendo are 15 years behind the curve then so it goes. Play copied games all you like and pull anything you like apart and mod it how you will, such things are fun. On "cheating is always wrong" then I am going to have to disagree quite strongly as there are plenty of occasions where it is perfectly acceptable. Try not to draw lines in the sand or oversimplify.