I could be wrong about all I'm about to say, but this is what I got from the story regarding those characters:
I'm assuming the only living people down in the dungeon are the player and perhaps the necromancer. Papin, the necromancer's apprentice, has been zombified, so is not technically "alive"
It's speculation, but I'm fair sure Papin is the only zombie on lvl 4 on account that the necromancer kept him close, so probably took him with him through the portal, and there are no other zombies anywhere in sight, only the skellies that belonged to the underworld "civilization" guards. Chances are he abandoned Papin while trying to escape Sir.
Hamon has probably never entered the dungeon, but yeah, he's the one sending more test subject to the necromancer, so he at least knows about it and it's exact location. Solid chance he's the author of the letter the player finds on himself when you start as "unknown", implying the player is just another poor sod sent to the dungeon on a bogus quest. That or
he's the necromancer!
Thaven appears to be a leader within the Guardian worship cult, or it's heavily suggested anyhow. He seems to know an awful lot about the dungeon and the Underworld, so he may have been down there at one time, but the necromancer's need to "send word to Thaven" from the Underworld confirms (or at least heavily imply) that if he's ever been down there, he's not at the time of the events of Exanima.
Anyhow, speculation aside, I can say for sure that the necromancer has been to the Underworld, altho it's possible he died down there, Papin was dead and zombified before crossing the portal (if he crossed at all), Hamon is a "facilitator" working with the necromancer and Thaven, and Thaven is a figure of authority to those 3 characters in some way but is not himself in the Underworld (or the portal facility), preferring to send his minions.