That would instantly vaporize faith in buying used anything, diminishing legit consumer's ability to resell as well, which degrades the whole point of physical releases. Its not going to be acceptable to consumers if putting a legit cart from gamestop into a legit system earns you a permanent console ban and cuts you off from your digital purchases. That would be a huge PR blunder and news fiasco even to people who weren't directly affected, because it could hit anyone buying a used game from anywhere other than a close friend.
What might happen is Nintendo blacklists a specific cart cert that has been duplicated, preventing you from running that game. Still a risk buying used since it might not work, but not one that will practically brick your system. Even then I doubt they are going to do this for people who make a personal backup and sell leading to a handful of duplicates out there, its those racking up the hundreds and thousands of duplicates from being shared online that would put a cert on the blacklist, and that at least makes sense if you are stopping that many people from pirating a copy at the cost of one dud cart.
Long term I bet Nintendo figures out how to detect the MIG directly anyway. Sky3DS didn't last forever, TX historically are only in to make a quick buck before things get tough.