There is a bug, that I don't know the cause of, that makes the rank 2 and 3 weapons not fire sometimes. Only the default weapon fires. The damage listed on the infocard will be the same because the way they're set up is that the Starbase gets all 3 weapons at the start, but you need to do the upgrade to allow it to fire them. So, the infocard will always show the damage for all 3 weapons, regardless of whether or not you unlocked them yet.

You would notice when it fires the others, however, especially the disintegrator arrays, since they're big purple lightning things. The bug affects all starbases though.

Not sure whats happening with you there... when i upgrade Vasari Starbase weapons, and ONLY weapons, i get the purple thingy disintegrator and missles with a noticable dmg increase ....  I only play entrenchment vs TEC AI due to silly mine spam and TEC doesnt spam mines as bad as the other 2, playing vs TEC means rebel attacks, to counter that i usually have a starbase at every planet i own and only upgrade weapons if i can afford it.... noticable differance between starbase with weapon upgrades and ones w/o.