Well I don't think it would really matter how much earlier SS takes place. The Great Deku Tree and all the Kokiri are most likely REALLY old.... at least, they can be simply because they all live forever. Unless there is specific evidence saying how old they are in OoT (which I'm pretty sure there isn't) all we can assume is that they've been around since the creation of Hyrule, which is most likely true, at least for the Great Deku Tree. Maybe not the individual Kokiri we met in OoT, but all I'm saying is it's still possible. IMO, the Great Deku Tree will make an appearance, but in "the land below", not Skyloft! How would he have gotten down to the Lost Woods from there? We could possibly see Saria, depending on how old she is in OoT, but like Ember Incubus said, obviously we can't see her explain her relationship with OoT Link if he isn't born yet!