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We know a lot about how they disappeared, though. There was a quite lengthy optional quest in Morrowind to learn as much as you possibly can. Most players didn't do that quest, for good reason. It was one of the two crazy Mages' Guild quests that the Arch Mage gave you, and he was insane. He simply told you "Go find out what happened to the Dwarves" without giving you any sort of direction whatsoever. Many players assumed this was a joke, but the quest is actually finishable. I'll admit I had to use online guides and such to find out how to finish it, but what you find out is actually quite a bit.

[Note that despite being formatted as an "interview" at the Imperial Library, the dialogue of all these people except Xan and Sinder Velvin is NPC dialogue from Morrowind. This is the dialogue you get when speaking to certain people about Dwemer, without and then with the proper books.]

i remember finishing that quest in TES3 and thinking the fact that there were dust piles and ghosts in the ruins meant they had destroyed themselves.. however these are not around in Skyrim so I am not sure

the most interesting addition to the puzzle for me is what Hermaeus Mora says about the Dwemer when i finished his quest, it is vague yet informed lol.. the dawnguard material is good as well but we're perilously close to losing the mystery

The ghosts would actually be a seeming contradiction if we assume ghosts and souls are the same things, but we get a few little lore hints scattered throughout TES games that a ghost might be only a part of one's soul, so it's plausible the ghost guardians of Dwemer cities and laboratories aren't the parts of their souls that disappeared.

i like to think that the Falmer cleaned the ashes away and destroyed all the ghosts ages before the Skyrim events took place.

yeah, interesting thought about them being parts of souls left behind. That's also what a lot of people believe 'real' ghosts are in real life