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Ganondorf did know. The fact that he did was integral to the very reason and method behind his plan in OoT; the fact that he didn't kill Link was also necessary for his plan to work, and for him to get all three fragments with relative ease.

I think I understand what the OP is asking. If I've got your post correctly, I think Ganondorf doesn't go straight after Link because he needs to make sure he gets all three pieces; this is why he bothered to capture Zelda after Sheik explained the importance of the Triforce to Link, such that...