If I remember, NDS carts have a limited amount of flash memory available specifically for saves, and only store one set of saves at any time. When it saves to the cart, it overwrites the data that's already there. That's why if you turn it off whilst it's saving, the save gets corrupt and you lose all saved data.
Emulators may have the option for sequential/backup saves, depending on the emulator. I've not used them in years however so I don't keep track of them anymore.
Interestingly, 3DS saves to the SD card for all the games I've poked around, and also include a backup save in there.