Well all those upgrades are massively expensive to max up, much more than a capital ship. Also realize that each upgrades is unit specific so its not like the universal upgrades from the tech tree. Factor all of that and the fact it cannot move the enemy could easily avoid it until he feels like trying to take it on.
1 last trick is for carrier spammers, to jump in while outside the range of his SB then release the horde of fighters that can destroy his own SB fighters and bomb it to peices. I've done it multiple times on multiplayer after I defeated his fleet, I just sit back while my bombers do the work. Also the max hangers for the SBs are expensive. Also the max upgrade limit for the SBs are too low.
The Vasari Starbase is worth it, due to the fact it can move and actively defend the whole system.