I've had this happen twice now. I've got 2 different villager bases set up one is a farm that allows the villagers to move around and farm land it is closed off with fence and glass over top and have had all the villagers disappear. I see no dropping of any mobs or anything. The other is closed off like a prison sort of deal and had no issues with them. All the villagers that disappeared were max lvl farmers and no way for mobs to spawn or get in. I was like 20 blocks away so I have no idea why they disappeared. Unsure on version just say 1.16 on my console