I mean the dwemer just vanishing was a mystery but i have a few theories. they may not be much but im not much of a theorie man. one is that like arniel from the winterhold story line they are actually still on this plane but just as shades and that's why their creations still roam protecting their ruins. Another one is they that they created their own plane. i mean they studied the daedra alot didn't they? Just a few guesses.....

I think this should be in the lore section...

Read some of the in game books, or do a search on uesp wiki

The theory that is generally accepted as true is, in simplistic terms, they became the Golden skin of Numidium.

The "Mystery of the Dwarves" have pretty much been solved by the fandom, though it's not officially stated.

Basically, Kagrenac used the tools Sunder, Keening, and Wraithguard on the Heart of Lorkhan, in an attempt to create an artificial god and/or turn the Dwemer to a pre-creation state. He, unfortuantly, miscalculated, and instead caused all Dwemer living on Mundus/Tamriel at the time to crumble to dust, and their spirits fuse to the Numidium.

this. Add to it the only living Dwemer left at the time was a transdimentional tonal mage or something, came back to Mundus and spent his remaining life looking for them, in nearly every plane of existence and still found no trace of them, finally contracting corprus and ending up with good ol' magister Divyath Fyr, and even he, a 4000 year old Telvanni wizard, who could clone versions of himself into "daughters" said the same.

How are there Dwemer spirits haunting some ruins in Morrowind?

Perhaps dwemer that died in battle before the use of the tools and the vanish of every dwemer.
I dont really know how ghosts work in elder scrolls universe.