I don't know what the case is for checking and downloading updates, but I wouldn't be surprised if it's the same as verifying before you can play online. Check out the write up by
SciresM. Basically the game card, or digital file, contains an encrypted certificate that is created for whatever medium you have. This certificate is 100% unique to the digital download or the specific cart that you can physically touch.
If I'm right and this information is sent up when you request an update from Nintendo, then they can very easily use an algorithm to determine if what you are requesting an update for is a pirated copy.
However, lets say if you own the game card. You should be fine to dump it and install it and play/update it with no issues. Though, it does seem the certificate has other encrypted info, so Nintendo could tell if it was originally for a game card and is now a digital backup. Obviously they don't do this yet, but they may be able to. If you end up sell the game card, I'd think you should be fine. However, if Nintendo sees someone playing the game at the same time as you, then they will likely notice it.
If the certificate has already been marked as banned and you go to update, and I'm right, you can consider yourself banned.
I'd bet that In these early times no one will be getting banned. In about a week or so, however, I wouldn't be surprised if people stop being able to get updates, go online, etc.
I'm not an authority on this information and this is purely speculation. Stay safe.