Since a Military Starbase does not provide active defence of a Planet or Shipyard in it's AOE (other than providing some stat buffs to ships) it isn't a complete priority to take out when attacking a Star System.
One way to enhance it's value and require Players/AI to commit ships & effort in attacking a Military Starbase before really invading a planet, would be to add Planetary Defence/Invasion Resistance modules.
Cheers,
Zoo