Well, I'm about to potentially take one for the team. My test 3DS arrived today and I will be playing games using the latest Sky3DS template file, NOT inserting private headers, in order to see if/when a ban happens, and if so how long it takes to happen. I will also be relegating myself to one single game per week with online interaction. I am fine with this simply because this would be a spare 3DS anyway, only taken out for on-the-road use or ad-hoc multiplayer.
I will also be potentially testing any theories related to a Nintendo Network ID being part of the ban, though if it gets to that point I'd need a volunteer who uses Gateway and can spare the time to flash a fresh emuNAND and take the information I provide to put it. Probably not the riskiest thing out of all mentioned but still, whomever would be okay with it should understand that it does involve a slight risk by association.
I will NOT be using any save data modifiers or anything else, because even if I could, it could potentially contaminate the experiment.
Wish me luck, folks. Hopefully this gets to the bottom of it a little bit more than where we are currently at. I'll keep you all updated.