I just realized something. There's always a large gap between Zelda games, something could easily have happened between Wind Waker and Breath of the Wild regarding the Great Deku Tree. The one in Wind Waker is the only one that looks completely different. Breath of the Wild takes the look of the one in Ocarina of Time. It's not unreasonable that either the one in Wind Waker is a young adult, and as the tree grew it changed shape. Just like a human does with old age. Something else could have happened that we don't know, and it could be a different tree entirely. Trees in real life can live hundreds of years without dying off.