I think that he's looking for Navi in MM, just as the prologue tells, 'cause he's kid again during MM, so he and Saria are still friends. (I suppose, if there's nothing to do with the fact, that Saria awakened as a sage, so I don't know did it afect it anyways, at least I don't suppose, but anyways...) And he knows, how to get to the Sacred Forest Meadow, and Saria was even shown along with all the other sages on top of the Death Mointain (well, Rauru wasn't in there, but why, it's a whole another theory...), in the end of OoT, so I think, what happened after OoT was that things returned to normal (To agree with my theories about this), and Saria wasn't never shown to actually disappear, 'cause just as I said, in the of OoT, she was there with the other sages (Well, not Rauru, but I've said that already about a million times...), but Navi really flew away from window within the Temple of Time, so she did disappear really.