The world transfer "delays" are server queues. These queues are important because they prevent too many people joining the server at a given moment and allows it to process sensitive character data in sequence. If you have a long queue that prevents you from reaching a hunt or fate, that is just the game's way of telling you that it has reached its limit for how many it wants to show up.

Mobs disappearing is not a server performance issue, but a client performance feature. There is a maximum Character and Object Quantity and sometimes at hunts this is exceeded, so characters or hunts don't render. You can improve this by setting it to Maximum in System Configuration and by having the game installed on an SSD.

Zone teleporting congestion seems to happen because there are player spawn points next to the aetheryte and these get completely used up when a hundred people teleport there at once. This is not really a bug, but more player spawn points could be added at aetherytes.

While these things could be improved, none of these things are bugs and are all working as intended.