I have seen small and missing eyes in half a dozen different species of snakes. Fortunately, none were mine, so I did not have to make the very painful decision to cull or not.
Nobody has figured out why snakes have these problems. As far as I can tell, there could be more than one reason. Genetics is a possibility, as in double merle dogs. But there could be environmental causes, such as a borderline vitamin deficiency in the mother. This sort of thing is known in various vertebrates from trout to humans. I would try building the female up with some vitamin/mineral supplements for a year before letting her breed in the second year. If she produced babies with bad eyes then, I'd probably not use her again for breeding.
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