i think basicly since his clothes got transported too and since shes always in his hat i wouldn't be suprised she'd get taken too while in his hat but that dosn't explain why she wasn't in his hat during the cutscene maybe because its two souls so when she got wrapped too shw wasn't warped to his location but near him on the floor?
In fact, Navi was bugging Talon - Malon's father - for years trying to wake him up. Endless shouts of 'HEY! LISTEN!' were not enough to wake the grumply old man from his sleep however. Perhaps Navi simply slept for seven years, due to the fact that she's constantly awake (like Link) and simply needed a good night's rest. Maybe she went off to join another fairy boy for seven years giving him words of advice such as 'WATCH OUT!'
Nah, I have no idea. I'm as clueless as you guys are. ;P