Kohaku doesn't believe in Destiny.
In fact, one would go so far as to say he defies Destiny. Or at least, he'd like to think he does.
One of the side effects of being resurrected, to him, is that you have to stop believing in mortal quibbles like Destiny, Fate, and the like.
He doesn't think it was Destiny that brought him into this world, that Destiny chose him to be one of those who came to Naraku's web, that he was chosen to murder his father and those people who were as good as uncles and brothers to himself, that he was chosen to be reborn.
Frankly, its because if he did, he'd end up hating Destiny even more than he did Naraku.
And right now, hating Naraku is about the only thing that keeps his body going.
He especially does not think that he met her out of Destiny, some star crossed nonsense about two children with unique (most would say impossible) circumstances that they, and only they, shared (well, there was an undead miko that could be likened to them, but they were different enough from her to be dissimilar).
It was chance.
It was fortune.
It was not Destiny.
But, when he remembers a sweet fruit and a sweeter smile, he will make it his destiny to meet her again.