In the Hyrule Historia, it is revealed that there are three timelines sprouting off of Ocarina of Time. It's revealed near the start of Ocarina of Time that the great Deku tree dies, leaving a sprout to grow and one day replace him. The original Legend of Zelda takes place in the timeline in which Link is defeated in Ocarina of Time, and the first dungeon takes place inside a tree in a secluded area, likely to be the remains of the Great Deku Tree. In the timeline of Ganon being defeated and Adult Link remained, the Deku Sprout grew into a new Great Deku Tree which we see in Wind Waker. It makes sense that Ganon would have destroyed the sprout once he gains control of the land.