While I agree that natural adaption would take thousands of years to happen. This is Hyrule we're talking about. Things happen a lot differently than in the real world. Also while not likely, there could possibly be a few Zoras in hiding, but the Ritos are without a doubt just the descendants of the Zora people. If you look at these quotes from Laruto (The Zora Sage), she says...
"You must find the one who carries on
my bloodline... The one who holds this
sacred instrument..."
"Nothing can stop the flow of time or the
passing of generations...but the fate carried
within my bloodline endures the ravages of
all the years. It survives."
So as you can see, in a single conversation she mentions a Rito (Medli) being in her direct bloodline. Which is pretty irrefutable proof that the Rito are indeed descendants of the Zora. Hope I helped!