To be honest, I don't think piracy will happen in the same capacity with 3DS games, if only because of the memory capacity. I may be utterly off-base, and even now I see it as superficial, but I bet one of the reasons DS flashcards are so popular is that you can fit 20+ good DS games on a single memory card. if each 3DS game is going to be roughly 2 gigs in the first place, it's gonna be a lot more expensive to buy a card big enough to hold a reasonable collection of 3DS games, which may help the situation.
Although, getting past a working 3DS flashcard and me actually buying one to pirate games, I'd probably just rotate them from my PC. So, self-defeating if you reason it out, but I know plenty of people (by which I mean "kids who think they're hacker-gangsta for buying a flashcard") who just wouldn't get that far.