If the doe ate it, it was probably dead.
Kits out of the nest: How does your setup/nestbox look like? A wall or lid the doe has to go over reduces the risk of kits being dragged outside on the teat, or wandering off. In nature the nest is at the end of a tunnel, downhill is always the way back, if that's not the case with a nestbox it can be a trap.
Predators: You wouldn't believe what small spaces rats fit through, some years ago I lost a whole litter to one, single rat. A wildlife camera is a very useful tool to see what's going on, you don't see rats - when you see them you have tons of them.