Nintendo hasn't sold devices at a loss unlike some other game console makers. At one point they were the only major console provider to make a profit on the device.
I think I'd forgotten that point. I also think they could just straight offer a second tier i.e. $10 for the device-linked game and $20 for the device-unliked.
IIRC, it was a huge issue for the 3DS. If you lost or damaged your 3DS, it was a real pain to get all your downloaded games back on a replacement device.
It's no problem since they introduced actual accounts (Nintendo ID). But you still lose your 3DS friends list, and games can only be installed on one system at a time.