A while ago, homebrewers found a way around Nintendo’s copy protection using the game Cubic Ninja . The exploit, in itself, wouldn’t allow people to, say, run illegal copies of games. It just allowed people to tinker with the 3DS firmware and write their own programs which, of course, may eventually mean that piracy would come about.
As a result, Nintendo has rolled out 3DS firmware 9.3, which should block the exploit. This will come as a big disappointment to people who were spending a lot of money on the obscure game just to use the exploit.
That being said, here are already “legal” ways to play backup games through the use of flashcards. So as far as piracy goes it’s just a limited measure.
Source: GBAtemp.net