Its a very valid point. However, while we have all seen/read of armored battle stations and incredibly large starbases in sci-fi, I dont think we have examples of incredibly well armored construction platforms. Would you propose the upgrades to be done via social spending, or military spending? (hence, tie up the shipyard while upgrading). In one respect, its nice to have a fairly important space based target, to be quite defenseless and fragile (they do have more HP than starbases however). On the other hand, yes, its quite rational to be able to buff its defenses if you desire so.
In regards to requiring larger ship yards to build larger ships, that's very interesting. It could instantly be the nerf for Colonizer building shipyards, as I wouldn't understand why a 1st gen shipyard would be able to build colony ships, but not medium hulls. Making the upgrade of shipyards to be 2nd or 3rd tier, to build colony ships, might cause quite a colony rush slow down (that is, until you have enough miniaturization techs to allow colony ships to be built on small hulls).