The sea is cursed, so the Zoras wouldn't be able to survive.

But yeah, it is really stupid, especially since Gorons somehow survived the Flood.

Welp, time to put my encyclopedic knowledge of nerd culture to use.
DEEP BREATH
Yes, Ritos are descendants of the Zoras from a time past, but their 'evolution' wasn't the result of a Darwinian style of evolution. The Goddesses, after flooding Hyrule to stop the King of evil, wanted to keep Hyrule a secret from the rest of the surface world. Naturally, the Zora, being an intelligent and sentient species that are gifted swimmers, could easily reach the flooded Hyrule and discover the truths that have been sealed there. To stop this, the Goddesses changed the Zoras into an avian species to prevent a return to the waters, and keep the sea lifeless until the time a hero would come. My reference is Hyrule Historia.