Dwemer got absorbed into Lorkhan’s plane of existence. Ghost fence was not made up of Dwemer souls. Dwemer spectres appear in Morrowind because of being connected to Heart of Lorkhan and the heart being used in a certain way but aren’t there in ESO or Skyrim. Dwemer did not get absorbed into the Numidium in the same way Arniel Gane did not get absorbed into the Dragon Born even though he can be summoned by the Dragon Born. The Dragon born can only summon the shade of Arniel Gane because the LDB (Last Dragon Born) was the one who heated the crystal in the convector. The shade can still be seen roaming around Winterhold College. That proves that it has not been absorbed into the Last Dragon Born.
Vivec and the other in the tribunal didn’t use Dwemer souls or ghosts to make ghost fence. They don’t even know where they disappeared, for all their Godly powers. In fact, the dwemer specters may just be a hologram that appeared because of Dagoth Ur’s use of the Heart in some way. Arniel Gane’s shade is also called a shade for a reason and not a ghost or a spirit or just Arniel Gane. It is just a hollowed out version. The real Dwemer are somewhere.