Well, there was rumors (very small rumors) rumbling of Nintendo or some other major video game company developing an anti-piracy system that does exactly that. Games would pretty much modify the firmware to reject all flashcarts, period. And without access to flashcarts, there's nothing you could do to fix it. Of course this is pretty much a low-class rumor that, if it were to be implemented, would only come in by the end of the DS lifetime. If it was used in this game, it would definately have more coverage than some random jackass parading around with false rumors.
Rest assured, you're commercial games are safe, don't worry.
Rest assured, you're commercial games are safe, don't worry.