Like you said, SBs really should get noticeable differences in appearance when you upgrade them. SB should also spawn rubble when destroyed.
Labs don't need guns, but I would like to see more customizable cap ships. I've heard that the next expansion will include this.
I agree, everytime you upgrade a starbase with a different tech, it should be visible on the starbase (just like TEC trading ports).
Giving labs the ability to "auto-defend" is not a good idea. That's why we have Gauss Cannons.