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.