Simple, but cheap, and not confirmed.
If he was aware of it in WW he could've just killed Zelda on the bed. XD Now that it looks like Ganondorf has been revived in BOTW2, it will be interesting to see if he gets back his intelligence and becomes aware of this.
Of course most of the Links and Zeldas are born different people; that's not what I'm disputing. Creating A Champion states that Calamity Ganon's hate for the hero and princess was legendary, yet he never met the ones in BOTW before when he sent the Guardians after them. The Links and Zeldas...
My conclusion is that Nintendo themselves don't know how the hell Link, Zelda, and Ganondorf keep appearing in different generations; they don't even know whether they're the same people or not, proven by the fact that they repeatedly and simultaneously say they're different from past...
Link is an incarnation of the Spirit of the Hero.
Ganondorf is an incarnation of Demise's hatred.
Zelda is a descendant of the Goddess Hylia.
What the ****???
The former two can keep on reincarnating or being reborn, but the latter can be destroyed. You would think the Goddess would've been...