If it’s just hatchlings, you can use liquid nitrogen to flash freeze them, if I remember the info correctly, this is only humane for very small animals, under 40g. Depending on the species and your access to liquid nitrogen, this may be a potential option.
For brain distruction, you can use something like a towel or plastic bag to avoid having to look at anything unpleasant, if that would make it easier. Breeders have also been known to keep animals like indigo snakes, king snakes or monitors to make use of such ill-fated hatchlings, they work considerably faster than a freezer, and it’s not as, for want of a better term, ‘messy’ for you, either emotionally or literally.
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