I believe that Ganondorf may have died, but his immortal form Ganon or his spirit escaped and is being reborn somewhere. How do you think Ganondorf came back in TP, which I believe is one hundred years after OoT...I think. So if Ganondorf came back after he was killed by the master sword, it is obvious that some part of him got away and was reborn.
But if you feel I am incorrect, then tell me what is wrong.
I think there is an interview in which Aonuma confirmed that Ganondorf died in TWW. I'll look for it...