Simple.
1: The last time Ganondorf saw Link, Link was an adult. So, seeing this kid isn't really going to prompt him to think "IT'S HIM!!!"
2: Ganon(dorf)'s return from the Sacred Realm is what prompted the world to be flooded, right? (At least, that's how it sounds in the opening story. For all we know, that threat wasn't even Ganondorf, but assuming it was...) Well, Ganondorf knows fully well that Link wasn't around then, or else he wouldn't be needing to wish for Hyrule to return.
And, basically, his attitude with Link at the beginning was "discard him". Which the bird did. He didn't care about this runt at all. (You'd think he'd learn, wouldn't you?)
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Well, everyone has a unique flow of their natural energies, so maybe Ganondorf can sense those flows so he knew that he was not the hero in the legend (The Hero of Time I mean). Its a possibility isn't it?
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That would explain one of the reasons why he knew Tetra was Zelda right off the bat.
