Because it's not? It's bound to your hardware as long as you have your hardware with you but if you break it or just change it sor some reason (like a XL) you can redownload all your stuff on your new hardware.
DD are linked to the hardware which is linked to your nintendo.com account. Link your new hardware to your account and drop a mail to Nintendo and tada, your stuff is back.
It's not as flexible as Steam or X360 or PS3 where you can login with your account at a friend's place, but it's in no way completely tied to your hardware with everything gone as soon as it breaks.
Still a hassle to go through to recover your digital download content if your system is ever stolen/lost/breaks.
Though according to a poster on GAF who is known to have inside knowledge, Nintendo is going to be retroactively bringing Nintendo Network accounts to the 3DS, so that should improve things somewhat. Whenever it happens.