I own two "retail" digital games: New Super Mario Bros. 2 and Fire Emblem: Awakening, mostly because their Streetpass potential is high and easily accessible when I don't have to switch cartridges.
I try to keep my 3DS in relatively good shape, and I back up my purchases on my external hard drive... but that still doesn't mean my purchases will be tracked. I worry about that, but I'm also confident in my ability to transfer all that material from my 3DS to my NEXT Nintendo handheld. So, if I continue to play safely, I won't have to worry about all these digital woes.
I don't know, I like the security of physical copies but the convenience of digital. I really wish Nintendo would make some damn accounts, though.