This makes me think that Vivec might be a little racist, or at least biased toward the Dunmer. All I am suggesting is that since he is the god of the Dunmer he wants them to be safe so that he can continue to be worshiped. It is possible that Vivec does in fact sense the Dwemer, but is simply lying in order to keep his position as God of the Dunmer. Maybe Vivec's disappearance during the Oblivion crisis was so that he might seek out the Dwemer for their more technological approach to Nirn so that they might help fight the daedra, which Vivec knows of the Dwemer have a hatred.
The Dunmer are racist, its sorta their thing. Remember constantly getting called "n'wah" and "outlander" when you played Morrowind? And of course it also plays in that Vivec is a Dunmer god, and that the last time he saw a Dwemer he was probably running it through with a spear.
As for whether he lies, its possible, but unlikely. We know what happens to him after Morrowind according to http://www.imperial-library.info/characters/trial_vivec.shtml, we have a pretty good idea of what happened to the Dwemer, and lastly the Dwemer didn't hate the Daedra by any means they simply refused to accept them as what everybody else did. The Daedra were a curiosity, a puzzle, they were fabrications (albeit ones with great power) - they were not hated, they just weren't gods.
One last note: as long as the people worship Vivec he can keep them safe, rather than vis-versa.