I don't see how this is any different than what Nintendo, Ubisoft and especially Square-Enix have done already. They write in a code that can tell when the original cartridge is in. If not fucked up shit happens. In some instances, the DS can't read the save data and won't be able to leave the loading screen because of it. In others, like Dragon Quest V and New Super Mario Bros., the game will glitch in funny ways to keep you from advancing, while still letting you play. In NSMB, Mario starts off as giant Mario and he can't be changed or get smaller ever, so once you hit the second level, you get stuck in the first section of the underground level. In DQV, there's a part when you first travel by ship where the game will endlessly sail in the ocean and never reach land. Shit is hilarious, but each ROM has a patch available within 24-48 hours of release that can fix the mistakes or has an Action Replay code that can fix it. This will be no different, just more of the same.
It is an annoyance though, because I like backing my games up and having them all in one place instead of carrying carts around like a doofus.
I do recommend everyone get a flash cart though. It has features the DS should have had from day one and still doesn't. Homebrew turns the DS into an incredible tool like an organizer, downloadable maps from Google, better web browser, IRC channels, e-book reader, comic book reader, music creator, MP3 player, movie player, electronic drum set, amongst others. Plus a few homebrew games have been simply amazing and better than many retail games, like Still Alive(a 2D version of Portal, just like the PC game) and Video Games Hero(8bit MIDI video game tunes from FF, Mario, Zelda, etc.) with Guitar Hero gameplay. It even works with the guitar grip that Activision made.