Yes! I've had the same issue! I've had about 20 villagers despawn from my world even while on peaceful mode. I am in the latest release.
Villagers are not the only entities of mine that are being deleted! Player-created iron golems and fed animals, as well as tamed horses have been disappearing on my realm. Each of these should never despawn, and yet they are.
Even named mobs are disappearing! Villagers linked to stations and beds, that I've traded with to the top level are disappearing as well.
@Shuminator I think that must be the issue, because mobs that are not in 1x1 holes are the ones despawning for me.