Miyamoto and his protege have been quoted as saying that this latest Zelda takes place 100 years after the events of Ocarina of Time. This world is actually the same as that world, just flooded. Event that happened in Ocarina of Time will be elluded to in Wind Waker.
That being said, Link very well may be Hylian again. During the time period where this flooding has occured, I'm sure the already existent people had to migrate to evade the flood waters and eventually set up the civilizations that will we soon become (all too) familiar with in Wind Waker.
Plus, bear in mind that this is another incarnation of Link, in spite of it being the same world. So, I guess we'll have to wait and see. I wouldn't worry though.