This bug doesn't happen 100% of the time, however it has happened to me a few times now. If you aren't looking at the name-tagged zombie villagers for the complete process of them turning into a villager, they sometimes just disappear instead. Yes, this happens even when they are safe from the sun, hostile creatures, iron golems, are name-tagged etc. I think they might be glitching out of the boat they're sitting in and then glitch into a wall around them and suffocate there, I'm not sure though. I have wasted quite a few golden apples because of this.
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Sorry for the delay, I just tested this using the setup shown in your screenshot, and the villager is indeed suffocating the the blocks. However, that's not because it glitches into the wall. Rather, the villager spawns on top of the boat with its head in the ceiling. You can prevent that from happening by making the ceiling 1 block higher.
Since the villagers are not despawning but actually being killed due to the design of the chamber, I am resolving this ticket as "Cannot Reproduce."
Are you curing one at a time, or two?