Aonuma had discussed this idea before, to varying interpretation. Many considered the following two infamous quotes to support the double timeline ideal, and they have only become more zealous with recent developments.
The first came in a summer 2002 Game Pro interview:
Q: Where does The Wind Waker fit into the overall Zelda series timeline?
Aonuma: You can think of this game as taking place over a hundred years after Ocarina of Time. You can tell this from the opening story, and there are references to things from Ocarina located throughout the game as well.
Miyamoto: Well, wait, which point does the hundred years start from?
Aonuma: From the end.
Miyamoto: No, I mean, as a child or as a...
Aonuma: Oh, right, let me elaborate on that. Ocarina of Time basically has two endings of sorts; one has Link as a child and the other has him as an adult. This game, The Wind Waker, takes place a hundred years after the adult Link defeats Ganon at the end of Ocarina.
Miyamoto: This is pretty confusing for us, too. (laughs) So be careful.
Followed by a similar (though better worded) comment on the Official Zelda Homepage:
In terms of the storyline, we've decided that this takes place 100 years after the events in The Ocarina of Time. We think that as you play through the game, you'll notice that in the beginning the storyline explains some of the events in The Ocarina of Time. You'll also find hints of things from The Ocarina of Time that exist in The Wind Waker.
There's also a more complicated explanation. If you think back to the end of The Ocarina of Time, there were two endings to that game in different time periods. First Link defeated Ganon as an adult, and then he actually went back to being a child. You could say that The Wind Waker takes place 100 years after the ending in which Link was an adult.