While I don't want to see a Dwemer DLC, and personally like the idea of them remaining "extinct," Sykrim should teach us that just because something disappears millenia ago, doesn't mean it can't return.
Take, for example, Alduin
(minor mid main questline spoiler)
Spoiler
We learn that through the use of the Elder Scrolls he was banished forward in time, appearing in the Fourth Era instead of being completely lost in the timestream.
Is it not at least possible that something similar could've happened with the Dwemer? That they tried to harness the powers of an Elder Scroll and something went totally wrong, sending the whole race hurtline through the timestream?
It certainly seems plausible to me.
I don't think we should treat it like it's completely an impossibility, especially considering that it's a complete mystery how they disappeared in the first place, and how sudden it was.