Hmm... well, in the beginning of OoT, the Deku Tree is narrating. He says, "Long have I served...". To me, this is sounding like he means he's already been around for a very long time.
If Skyward Sword is before OoT, then it's possible that the Deku Tree might be present in the game, maybe as a younger tree. And, if he is present, then it'd make sense that the Kokiri would be as well, seeing as they are created by him. As for their role I am unsure. They didn't have a large role in OoT, more of a presence. I think it can be similar in SS.
Or, there is the possibility that a Deku Tree will be present, but we never actually see it or the Kokiri Forest. Remember, people don't enter that area. It was rare for Link to be there, but that was due to extreme circumstances. And, people who enter the lost woods (which is like connected to the Kokiri Forest) don't make it out as humans....
So, even if its possible that a Deku Tree would be in SS, I don't think we'd actually see it. I can't see a reason for Link to go there, especially since he's from Sky Loft, and not the same place as OoT!Link.