I added a beam interceptor and a protective field to my starbase. I fought several battles within the radius of this base. During combat, enemies were able to inflict full damage to my ships. Also, in the after-battle report, I noticed that I did not receive any starbase bonuses. Oddly enough, I have fought battles within enemy starbase range that indicated the enemy received these bonuses.
This is sort of an unfortunate bug, since I thought one of the neatest features was the idea that a starbase could add bonuses to ships, adding a very cool "fort" feeling to the game. Alas.