Well, you know, Pokemon cheaters don't bother me at all so it's not a problem and so I don't really understand what answering so seriously.
Hacked pokemons or not, in battle, there all at the same as you can't outpass the game limits for the stats, moves and such so I don't really care at all (those peoples just spare some times by not having to breed them manually). Same for Shiny, I have nothing against people who hack pokemons to get the shiny colors. People who do shiny hunting mainly don't do it for the color, just for the pleasure of the hunting.
And you can't now the IVs of the opponent pokemon anyway, so no one could say a shiny legendary have 6 IVs, just guess at max.
The fact that something can be done don't mean most of the people manage to do it. You can get rich, it's a fact, but most people never manage to get rich, for example. I managed to get a side effect of a medecine which only had a 0.00001% (1/100000) to get so I know everything is always possible, but still, the fact I managed to hit badly such a probability don't mean it's not pretty rare to get th same side effect.
Yeah I've tried everything I can think of, I'd change my mac address on the 3ds if i knew how, if thats even possible. It seems pretty clear to me it's a unit ban. Yeah I'm not even sure that person was banned to begin with, came across like he read up on the error code and was all "oh they just can't connect, I'll say i have the same error and i just reconnected" but thats just my person opinion, he seems to be the only person with a private header who got banned and also then fixed it.
Are you on 4.x or 9.x for the sysnand?
If it's 9.x, can you try a game that not require updates on sysnand to see if the whole system is banned or just emunand?
If you are on 4.x, maybe try to save your emunand with "emuNANDTool_1.0.1.exe" then try to format it to check if it change something? (dunno but the ban could be related to the friend code? Which is different from sysnand if your emunand is not linked with sysnand, basically from what I remember both are the same linked and when you unlink them, the format of sysnand change it on sysnand).
Edit : Read on a previous message that both are linked so yeah, if it's a friend code ban, sysand wouldn't work either way. Personally, I would still try to backup emunand first (in case you have some games or other things you want to backup), then I would try to format sysnand (without the SD card inside the 3DS which would unlink the emunand, it'll ask to connect to internet but won't update, then it'll reboot, put the SD card back in, do the configuration and it's done), then I would try to format emunand and update it again and check if I'm still banned with a retail game in classic mode. If it's not working, it would mean it's a ban of the 3DS unit directly, and if it's working again, it would mean it's a ban of the emunand/friend code.
What I find is weird is on other system, 360/PS3/others, when you are banned, you are banned from everything, even the shop, so they really are units ban there. But if you would be banned from all Nintendo servers, you shouldn't be able to access the eshop. Same if your NNID was banned.