This is a subject I've put a great deal of thought into... The Zoras have in fact evolved in Wind Waker. However, I believe it was not over a long period of time... but rather quickly.
Why? It makes seemingly no sense... in a world of endless ocean, you'd assume the aquatic people of the Zora Kingdom would thrive. I'd say... perhaps not.
The Gods sealed away Hyrule for a reason. I believe, in order to ensure its existence remained a secret, the Gods transformed the Zora people into the Ritos we see in Wind Waker, giving them a new Diety to worship (Valoo). The transformation was likely gradual yet quick, and in the interm the Zora/rito hybrids likely developed the Grappling hook as a means of transportation.
Natural selection simply can't work in such a short period of time... (200 years is way too short) The gods must have set their change in motion personally.
Also, had the Zoras still existed, Jabune likely would have a society built around him. Great Fish Isle did have traces of a civilization, yet if you look at the ruins, it is clearly that of above ground cottages... not the accommodations the water dwelling Zoras would prefer.
The transformation of the Kokiri is also the work of the Gods as well. The tips of mountains are not particularly full of vegetation regularly... It was their duty to make this so. Bring life to the mountain tops.
The Rito too, perhaps changed for a purpose as well... and that is to act as a unifier between the survivors of the great flood.
That being said, this is all speculation, but I find this to be a rather reasonable possibility.