They haven't hacked the console yet. They simply using the backwards compability of 3DS to play DS games and use that to run DS flashcards.
The reality is, the actual security to play 3DS games and not DS games has yet to be cracked. That's the important one.
In the end, this hasn't affected Nintendo sales one bit in the past. So even if it does get cracked, this time around, Nintendo can simply auto update without the users consent to close any security gaps as 3DS was intended to do so.