I was also a bit annoyed that the Trisolarians could mass produce these godlike sophons and never thought to use them to find non-inhabited solar systems to colonize. The third book did slightly explain this by having regions of space that broke their connection to home, but if you can produce thousands or millions of these things it doesn't matter so much if you lose some.
The logic of "in order to prevent other species from using up the resources in our universe we have to destroy the universe" never really worked for me either. The third book had a low level flunkie in an alien race launch an attack that would doom the entire universe at the speed of light with only the approval of a low level middle-manager. I'd almost say it was a parody except that the books took themselves so seriously.