Because the 3DS CAN play DS games natively? Whether or not it plays 3DS roms is irrelevant. Going by your logic, it'll be ok if I make a phone app that gives you unlimited texts (Whatsapp doesn't count because it uses mobile internet) because my app cannot give me free calls. O____oGee that's funny, last I checked current flashcarts can only play DS games and couldn't ever be used to play 3DS games. So how exactly are they "protecting their platform"?
Sure Ninty can't stop you from using it on your other consoles. They prob would if they could. I like to think like a lock on the door. The hardcore/determined thieves/robbers will break into your house even if you put 6858365838572909028473674 locks. But that doesn't mean I am gonna leave the door unlocked. Gonna put SOME sort of a fight in that sense.