Several causes of this issue been fixed:
- Zombiefying a renamed Villager would not copy the PersitenceRequired-flag
- It was possible that a nametag appeared to have been applied while this was not actually the case for the server.
- Mobs in boats disappeared when they were saved in a different chunk than the boat
With the amount of duplicates this issue has it is entirely possible that there is still remaining issues of entities disappearing that have not been resolved. However these are most likely not related to nametags and despawning and should be tracked individually as their own report with context and if possible reproduction steps.