The 3DS is not going to have an HDD... period. Too many moving parts, too much risks of damage and data loss, and you could not play a game that requires you to shake the 3DS to perform an action as that would cause to the HDD to malfunction.
No manufacturers were interested in Toshiba's small HDD's because of the lack of space and high cost of initial development. My Archos Gmini 402 Camcorder had a 20GB 1.8 inch HDD and it was a great device... except I could not go jogging with it (good by all exercise games on the 3DS), and I could not have it playing in pocket on a hot day or the entire device shut down because of how hot the drive got. Towards the end of it's life the HDD became unstable, constantly losing songs and videos, along with annoying playback errors, and me frequently having to reformat the drive, and then upload my files onto it again. Don't get me wrong, it was by far the best PMP I have ever owned and I haven't owned one since then but the device was ruined by the HDD.
HDD's are the past. They may be getting denser, cheaper, and faster, but SSD's are catching up in all of those categories, although the cheaper part is taking the longest to catch up.