So for about a month I have lived just outside of a village, and just recently most of the villagers just disappeared out of nowhere. The only villagers left are the ones trapped in their homes with the job block replacing the door and the one without a home that just wanders around the whole time.
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There is one villager who doesn't have a house (since I removed the bed) and he is still there, plus the game is on peaceful so no harmful mobs will spawn.

Having the same problem. On peaceful and all villagers despawned

Starting to get this issue as well, but only since the 1.13 update. First my villager breeder guys disappeared, then I noticed all but 1 of my iron farm villagers have vanished. All these villagers were protected with no physical way to get to them other than breaking blocks and all the blocks are still in place. Without the breeder, i need to travel over 1000 blocks to get new villagers for the breeder to fix my iron farm, as when I went to any nearby villages, they all got killed by the pillager raids going on.
The fact that all your protected villagers are still there strongly suggests that your unprotected ones were killed rather than despawned.