Also, there are physical versions, and those aren't really linked to the eShop.
Carts are different, they have their own cart-unique header (that is why Gateway players that use a "public header" get banned); perhaps they now also check to see if the header was issues for the game in question.
That being said, let's take a step back and review the situation, considering you have a "hacked" 3DS and a separate 3DS on OFW etc. for eshop purchases, etc. It's not wise to spend $400+ on eshop purchases over the years and then do stuff that might p*** Ninty off and have them retaliate against you. So have a street-legal system with your "old" NNID and purchases, and a hack system with a burner NNID and no purchases.
Now what does a ban do to you?
1. Cartridges
They'll work as always.
2. eShop/CIAs
You can download and install titles, DLC and updates unofficially the same way as before.
3. Updates
Don't know if you are also banned from installing firmware updates, but if you are, all we need is an updated version of SafeInstaller and you can upgrade to any new firmware Nintendo puts out.
4. Online play
This is where the real problem lies. Do we really want to 'fully hack' access to the official Nintendo servers? I think not. The people that used to have Sony PSPs may remember the same problem. Coldbird and the PRO firmware team came up with a way to use (an) unofficial server(s). Perhaps that's the way to go. Since B9S/sighax allows for CFW, perhaps a "pro online plugin" will take care of online play. You can only play against other "pro online" players, but there seem to be enough banned people around nowadays to make this viable. I mean, if your 3DS is perma-banned, anything is better than nothing.
5. Streetpass etc. (Ad-Hoc Mode stuff)
Same as 4. Not sure how damaging a hack would be (so you can interact with people with non-banned systems like usual) but perhaps this can be customized as well. Anything that doesn't require an active Internet connection we should be able to circumvent any bans unless Ninty starts distributing large blacklists.