Villagers despawn randomly. So far there is no way to replicate the conditions as there doesn't seem to be a reason for them. It appears to be random however there might be a correlation between logging off and back on again or leaving the area and reentering but might also be coincidental. Villagers are always perfectly well protected meaning there is no chance they were killed by other mobs or struck by lightning, further confirmed by the fact that other villagers in the same area remain while a few of them despawn. If attacked by zombies all villagers in the area would get infected and turned instead of just one at a time, and if struck by lightning there would be witches in the area.