I asked about this same issue in a "game talk" thread. Then I raised it in a bug thread. (Search for the word "unarmed" if you want to see those.) You're not the only one.
You might answer a few questions for when someone eventually looks into this:
1. What version are you running, 1.1?
2. Is this happening in a campaign scenario, and if so which one? Or a regular "sandbox" game?
3. What difficulty did you have it set at and what intelligence level was the enemy set to? (I don't think this affects the problem you're seeing, but others will ask and assume you're mistaken and imply you're playing on super-easy and choosing to fight brain-dead opponents.)
EDIT: Whoops! Your subject line answers two of my questions: The difficulty level and that it was scenario 2 of the campaign. Sorry I overlooked that.
For me it happened in several campaign scenarios with 1.1beta4 and 1.1. I don't know the cause or how to fix it. I think that it might only happen in campaign games, or there would be more questions about it. It's also possible it only happens to people who updated with the collectors edition content or something (I did that, and I'm sure not everyone does.) There was some speculation that it had to do with the rate at which the AI designs new ships - that they aren't doing this often enough, and so aren't building ships with weapons. I don't know if it's true, but I thought it was an interesting suggestion.
I think I'm going to set the game aside for a few months while they stabilize it.