The updates haven't been banned as no one has pirated games yet.
Now games are being pirated that changes everything. In the case of the BBB titles, there hasn't been many people using them.
Once Nintendo starts getting 10,000 requests from the same game cart is when bans will happen. Scries did say that even when you play the game offline it registers the cert, then when you go online the certs are uploaded, to give you your eShop coins.
Updates have nothing to do with it, the first time you put the cart in and hit play it's now in the q to be told to Ninty you have that game with that cert.