Maybe but not as likely as you would tend to believe. I played both Pokemon Sun/Moon as well as Ultra Sun/Ultra Moon before their release dates while never wiping my play history. If I recall correctly, the only people banned for playing those before release also went online. At the very least, a manual check would have to be done to see when the playtime started in comparison to its release date which sounds tedious what with millions upon millions of users to check.
I most definitely have to start asking if people are using this. However while I have not fully read up on their EmuNAND, it not only seems dangerous from a banning perspective (splitting the NAND?), but it also seems like it may brick the console (seriously, splitting the NAND?)