These are still lizards being lizards though. All that they've done is had some minute changes in jaw hardness, head size, and stomach size. That is hardly evolving from fish-men to bird-men in a few hundred years. Also remember that since lizards don't live as long, their generations are shorter. Since we know that the Zora age at the same pace as Hylians and humans (Princess Ruto hasn't aged much more than Link has in the seven years between time periods in OoT), so we can assume that a human generation is the same as a Zora generation as well.

Since human generations range from 20 - 40 years, at the very most, only 45 generations of Zora have occurred (assuming that all gens between OoT and WW only consisted of 20 years, and that since we don't know how many hundreds of years have passed, but clearly not a thousand, else Aonuma would have used the word for thousand, that there are 900 years between the two games) to at the very least, 2 1/2 generations (40 years gens, only 100 years between games).

In your article, it says that what happened to the lizards happened within 30 generations. So, even if we take the absolute maximum number of generations of Zora that could have occurred between OoT and WW (45), there is still just no way that they turned from fish-men to bird-men in that time. Oh, and to those trying to make the argument that all the Zora had to do was become permanent land dwellers because they get their wings from Valoo, consider this.

For a bird to fly, it has to have the proper bone structure, and more importantly, the proper bone weight. That is why birds bones are hollow. So that they can fly. Even if all they had to do was make it to land, why would they have needed to have hollow bones unless they needed to fly, which means that once they got on land with solid bone structures, they would also need to evolve to have hollow bones, thus making the time between it even longer. So this whole argument about only needing to evolve onto land is a little far fetched.

If these water monsters became too numerous or too powerful for the Zora, it is far more likely that they would have evolved to be stronger fish-men, died out completely, or left the area of ocean that was endangering them than evolve into bird-men. I'm sorry, but your hypothesis just holds no water.