Okay, the theory about the Maku trees being Deku saplings planted by the Koroks actually makes sense. I think that part's great.
But I don't really think it says much about
The Wind Waker's placement. Unless of course anybody has any indication of whether the Koroks existed before the flood or not.
If they didn't, and only Kokiri were around before Hyrule was flooded, then you've got a decent theory, here. Otherwise, the trees could have been planted at any time.
Spoiler (Highlight to read):
Personally, I put the Oracle games sometime after A Link to the Past because of Ganon's resurrection. If he was resurrected, he must have been dead, and he was killed at the end of ALttP. That being said, I put The Wind Waker after A Link to the Past because Hyrule was destroyed at the end of TWW, but is obviously still around in ALttP.