Hey I want to join in, someone on reddit made me look into the issue a bit.
I've never installed those behavior changing mods, i've only runned small mods before. I tested it myself by hosting the server and playing on it. In short : it happens on vanilla don't try to blame the user for it. (Even though there's always been bad user reporting, you should not say that it's the user fault that actively (i'm a dev myself).)
I've had the issue happens to me by playing on default server rules, without any mods, just shout once or twice in a city and move a bit and you'll see zombie despawning. It seems to happens most likely when they're quite a few of them (not saying a hundred or more, juste few dozen is enough)
Note : I was actively trying to check how it happens, on normal gameplay i'd have gone away, or would have avoided having that much, or would have fought them (so the issue would have happened but I wouldn't notice it).
In regular gameplay it actually happened from times to times when playing with a very short list of mods such as "Unclear moodles" and few others (nothing that change items or anything). The most regular version of the despawning for me is freshly killed zombie that gets removed. It happens few time by game session (host hasn't port-forwarded, so it goes through the steam thing), when several player are around killing a group of zombies.
From the videos and what I understand I guess it's most likely caused by zombies being desynced between the player and the server. Once the zombie stop following the player, I believe the player doesn't "own the zombie" locally anymore (am I wrong ?), and the remote server doesn't update it because for the server the zombie shouldn't actually be there. I might be quite wrong about it but I don't know why it'd happen otherwise.