I just remembered that certain quests required it (Tree surfing) so I was concerned. Plus it was always a lot of fun to jump up and go exploring.
It's possible to use a treasure chest, crate, etc. as a little boost to help climb up the town wall. Some crates or barrels from Toad Village are enough to get atop the trees near the Oracle cavern. So there's still some possibility, even for a short character!
Hmm..all the quests I can think of (that require sequence breaking due to improper order [seed quest]) can also be solved via Vanishing through the tree walls. Of course, it can be time consuming finding the appropriate weak spot in the trees. But once found, these spots are a good time-saver for later playthroughs.
[(Warning, Spoilers!-->)] NorthofA'sShrine and trees totherightofTorin, for example. [(<--Warning, Spoilers!)]