After a 36 minute call to Nintendo, all they could say is that I violated TOS, I had to convince them I purchased the games legitimately through Amazon, thus it comes down to the whole "unauthorized software" thing, which of course they don't go into detail about. After further evaluation, the common link with these 3 banned N3DSes is that they played Pokemon Sun, specifically one had the ROM running through Gateway.
My theories on why I got banned.
1.) Using a patched code.bin/.ips, going online with it. Namely SciresM's original patch, and just an ips version of it for testing. QR code patching and no-outlines, maybe the latter triggered Nintendo's ban.
2.) Using PKMN-NTR to live edit the game. The edits would be live to the point of say I trade the requested pokemon with someone, and I realized I made a mistake. During the trade, I'd edit the pesky pokemon, clearing up the errors with it. This is something I've done in the Gen VI games, so this is another theory with no precedent. The common thread also just so happens to be N3DS, whereas O3DS consoles, no issues.
3.) Gateway, perhaps using the ROM in one system, which had a much older save of the one from the cart, was an issue. Going online with that particular game at the same time as the legit cart, that's a strong theory. After all, I started this just 2 days ago. Hmmm.
Lastly, the woman said the bans on two of the consoles are temporary, she couldn't say about the one that never went online with the Gateway ROM, and also the most important console due to the NNID having Pokemon Bank. Again, this is just the 002-0102, I haven't gotten the NNID ban. From what I read, the ban is supposed to last 15 days, but she didn't tell me that, she didn't give an exact window of time, so basically I have no clue when the ban will be lifted. The solace is that it's temporary, and my immediate action is to change up the Gateway method. Again, I did it solely to speed up the GTS request process. I mod for a subreddit that's getting flooded with Gen 7 GTS requests, doing them all off one game was getting to me, I figured going to the ROM will help, on another console. Instead I should either restart the ROM, new save, or start up Moon and make it to Festival Plaza, whether it be through the legit cart I have, or the ROM. With this ban though, I'll have time to play through the legit cart, so this will most likely be the immediate action to take.
Calming down after the phone call, I won't deny I violated TOS, I pretty much have been doing that for 2 years, everyone here has basically, through homebrew or CFW usage. Doesn't mean pirating, I never went online with the leaked SM games for instance. What's bothering me is not knowing the reason outright, so I could avoid doing it again, all I have now are these three theories. For my patience, I'll assume number 3 is the culprit, Nintendo was able to nail the fact that those three consoles have been using Sun, ban. On the other hand, today I got online through an O3DS using the Sun cart, and while I can still go online through that, if that gets banned too, I'll know for sure that's the culprit. Of course, I don't hope it gets banned.
I don't know about requests for the time being, I was thinking of not doing them at all, but without knowing the time span of the ban, I may have to just keep at it, in a slower, more restrained rate. Seeing as there's no ban wave due to these specific theories, I'm convinced it's isolated, not a blanket ban, the fact it's temporary says as much. Perhaps I do deserve a stern talking to for doing this, being a bad boy to daddy Ninty. The thing is though I hack Pokemon for people more than I do myself. Currently on Sun I'm soft resetting Solgaleo, and have not resorted to hacking a Catcher Smeargle or enabling a 100% capture patch, bred an Adamant Syncrhonizer Abra legitimately, catching a legitimate Ditto. It's a habit to play through the story without cheating at all, and then do a bit of this and that afterwards. Yes I've used PKMN-NTR to read IVs of the Solgaleo, but you can basically do that legitimately through an IV calculator, you get a bit of a range as opposed to exact values, but still.
Just saying, not the stupid pirate that got his/her ass banned for playing the games early and going online with them. I'm the somewhat stupid person for doing number 3, I could've just fired up Moon and make it to Plaza, and even edit the save to have the Dex complete, or not do that part, I can get by without it. I don't think 1 or 2 caused the bans, they're theories though, I think 3 is the most likely since it really comes off the heels of starting it. I'm expecting a call back with more details about the ban hopefully. They said they'll contact me and will e-mail me the TOS, as if I need it.