The programs can be generated through qr codes though. You could have a program find a rom file and put it in qr code form allowing it to be scanned and downloaded.
Also it wouldn't be a hack. It would be using exactly what the program entails.
And you honestly think they won't be heavily policing and removing ROM hacks, even if that's the case?
I think you're forgetting that this is DSi ware, not 3DS ware... so there's literally nothing new at our disposal that DS flashcarts don't already give us, even if this does allow for hacks.