First, the question wasn't, "When does the game take place?" The question was, "Does the game take place before or after Ocarina of Time?" Wind Waker is a few hundred years after Ocarina of Time, so it's fair to say it comes after. Also, it's not hard to retcon it so there was a hero between Wind Waker and Ocarina of Time, especially if the people who told the stories that became legend were unaware of the hero's existence. Link will appear to jump back and forth between the distant past and the distant future, and the dystopian future might be after the Hylians fled to the mountaintops but before the flood. I can think of a dozen ways there could have been a hero between OoT and WW. If we were to exclude WW prequel though, that doesn't exclude WW sequel.
Second, with regard to what I said about the Rito and the Koroks, the existence of the Rito is contingent upon the existence of Lord Valoo. Lord Valoo was born on Dragon Roost Island after the flood.