The commercially available "snail-rid" products rely on copper to kill snails. I would not use any of these products with fry present.
I do not know what type of snail you have. The most common snails with which I am familiar will not harm your waterlillies, but will eat dead, dying and damaged leaves. (There are apple snail-types that will eat any vegetation, but these are rarely transported on plants and do not reproduce until quite large, so I do not think they would be a cause for overpopulation in your pond.)
I'd suggest physically removing as many of the snails as you can without too much trouble and leave the fry alone. They do not take handling well and you're sure to miss a bunch in a pond with plants. As koi grow, the smallest snails will be eaten, and gradually larger ones. Think of the snails as a supplemental food.
Of course, you may have a type of snail with which I am not familiar.