She doesn't, that's just a structural thing. Right now her armaments, (preliminary) are three small missile harppoints, 2 small energy mounts, and 1 medium energy mount. She's kinda similar to the mule. Slightly faster and with a slightly bigger cargo hold, but not as well armed and less durable.
Anyway, having gone over it, the ships in at least some of the big fleets are indeed not receiving weapons like they should, while smaller fleets are. I've turned on the debug in the variant selector but it's not reporting anything wrong. Very peculiar. I'm at a loss as to what's wrong, ao I may have to resort to disabling the randomly selected variants, which would be a shame.
Edit: Okay, I think I've determined the problem. It seems like fleets which are spawned while the player is outside of the the star system do not get randomized, so they spawn as just the basic, unadorned Hull. I think this should be fixable. Double edit: Wait, I'm being stupid, it's probably just I forgot to add the randomizer script to the self defense force. Derp.