In my current game, I have a custom opponent with the Thalan personality, but not their tech tree, using missiles. This suggests that if this isn't one giant coincidence, whatever's causing it is probably related to the Thalan tech tree.

I'm not finding that this really hurts them, though - typically, it seems like beams are a minority weapon in most of my games, which makes this an advantage for the Thalan, as less races are likely to have defenses against them. (Of course, the shoe is on the other appendage when beams are a dominant weapon type, but that doesn't seem to happen all that often).