The current lore doesn't hold together.
The Dwemer wished to equal or exceed the gods/aedra/daedra, not to extinguish themselves.
Thus, the current theme that they integrated themselves into the skin of the Numidium, lost their individuality and transcended to a higher plane as a perfect 'nothingness' simply makes no sense. It's like assuming that they concluded if they suicided their race, no one could claim to have defeated them. That is so illogical that it forces the dismissal of the entire 'transcendence' hypothesis, which is after all just based on lore in books from the ES series that was 'written' by characters who were simply speculating on the dwemer based on scattered, paltry evidence.
This leaves only one conclusion, the final conclusion that cannot be escaped:
They are still around somewhere.
Ya just can't get away from it. Everything points back to that conclusion.
Thus it is GUARANTEED that the Dwemer will reappear - and it will be devastating.
Creation in the Aurbis is subradient.
From Anu-Padomay to Et'ada to Aedra to Ehlnofey to Aldmer to Dwemer.
"It was unfashionable among the Dwemer to view their spirits as synthetic constructs three, four, or forty creational gradients below the divine. During the Dawn Era they researched the death of the Earth Bones, what we call now the laws of nature, dissecting the process of the sacred willing itself into the profane. I believe their mechanists and tonal architects discovered systematic regression techniques to perform the reverse -- that is, to create the sacred from the deaths of the profane."-Baladas Demnevanni.
Instead of being lots of little souls, fragmented and small, they intended to form one oversoul.
Instead of creation being an inevitable downward spiral, they sought to return to the greatness of before.
Not mer, not Aldmer, not Ehlnofey even, they intended to transcend the Mundus itself and return to the glory of pre-creation.
Dwemer metal, incorruptible and timeless as it is, is a step towards that, as it is created from mortal souls.
The Numidium was the next step.
The real question is not what happened to the Dwemer, it is why Kagrenac ultimately failed and why Numidium did not come to life.
One theory states that the Triune deactivated it as it was still in the process of activating itself.
I believe that they did succeed, but that their Numidium is temporally reversed compared to our timestream and thus inperceptibly walking back towards the dawn.