Yup it adds a +3 to that for a total of 6
Not quite sure what you're referring to, but if you (or even better, Stardock) removes this line from Improvements.xml:
You get a building, called Orbital Defense Platform, that adds 50% planetary defense and +3 adjacency bonus for ship building. There's no additional fighter cap added. This matches the in-game description.
Since there is no building called "PlanetaryDefenseSystem" it never shows up. Seems like a bug. I hope they fix it.
(I'm playing Crusade, not sure if its different in the base game.)