Morrowind had plenty ofhttp://www.uesp.net/wiki/Morrowind:Dwarven_Spectre#Dwarven_Spectre wandering around what was once their homes and attacking anyone who dares trespasses, so why then is there a lack of them in Skyrim?

Could it be the vengeance fueled by their defeat at Red Mountain and a supposed Chimer involvement in their disappearance which causes them to roam Morrowind to punish the Dunmer, could it be that they fear the remnants of their Snow Elf brethren whom they tormented and enslaved for so long or could it be the infamous 11.11.11?

Many things have changed in TES. Maybe it was just cut in-favor for the machinery which is more interesting than ghosts.

For lore reasons, I'd say that with the "destruction" of the heart even the lost dwemer souls finally disappeared.

For gameplay reasons, 11.11.11.

Or maybe they might have them in a DLC

*Kills you for mentioning DLC and traps your soul in the Soul Carin*

Thanks to Skyrim's exploitative mechanics I'm immune