You're overestimating the size of the pirating community. You're talking about pirates (maybe 10% of 3DS users, tops) that are willing to spend money on a game (drop that down to like 2%). These are made up numbers, but really think about it, not everyone out there is a pirate and not every pirate is going to buy a game for the sake of dumping a header.
On top of that, as I said in a previous post, Nintendo probably has a way of distinguishing a real cart from a GW/Sky3DS by now. I don't think they would be banning people without definitive proof of them using a pirated ROM onine. There are plenty of ways that Nintendo can use to check, including mismatched headers. Judging by the way their developer program is locked down, there is probably an allowed range of headers for each game that Nintendo licenses (every game on 3DS), and they definitely keep track of which game uses which range, otherwise there would already be unintended duplicate headers from multiple developers.