I didn't read all of every post in this thread because there are many very long ones, so I apologize if I am rehashing something I missed while skimming:
I think it is a good thing that starports are defenseless, they don't take that much effort to defend. The are also very cheap to build, so having your starport destroyed shouldn't set you back that much. That said, there are some legitimate concerns about the current design that I have seen raised. One is that defending starports is something you have to teach players to do. Starports, especially those near the edges of your territory are very tantalizing targets, and I think players in general tend not to play 4x games super defensively. This is not a flaw in the game, but a conflict between fun strategy and good strategy. It's smart to use your first few ships to defend your starbase, but it's more fun to send those ships out exploring or threatening your neighbors' stuff. Furthermore, if your economy will only support a small number of ships, it's kind of a bummer to have to have them docked rather then doing cool ship-stuff. The second problem I see is that having all your starports destroyed makes you unable to produce ships to defend yourself. This seems like it is only a problem very early game, as once you have 3 or 4, you will be able to produce ships at the others to counter the fleet that destroyed your starport. If your enemy has enough strong fleets to keep all your starports neutralized, you were probably screwed anyway.
Anyway here are some ideas that might address some of these issues without giving starports weapons.
1) Make starports require ground soldiers to conquer: Say that starports are such massive and sturdily build structures that they can only be destroyed from the inside. Therefore, in order to take out a starport, you need a transport to bring soldiers to board and destroy the structure. Unlike invading planets, the surviving soldiers would reboard the transport after the destruction of the starport. Starports could also build a project that would transfer population from sponsor planets to the starport as military personnel who would defend the starport in the event of a boarding. This would introduce some interesting gameplay, as well as delaying when starbases could be destroyed until an certain tech level is achieved.
2) Require a special module to destroy starports: This basically the same idea as #1 but introduces a new mechanic rather than adapting an old one. Say that starports are protected by massive shields that are invulnerable to conventional weapons. In order to destroy the starbase, you need to have a ship with a special EMP torpedo module disable the shields first. This module would be very large, making the ship that carries it much less effective in combat, and perhaps even requiring a cargo hull.
3) Make ships docked at a starport maintenance-free: This is a less drastic adaptation, but would encourage players to dock ships at starports and not make them feel like like they are wasting the few ships they can afford to maintain if they don't have their economy humming along yet.
Just throwing some stuff against the wall, what do you think?