Well but shields are useless in subspace and when the ship explodes during transit, especially with 5 reactors (remember, they had to fill the Bastion's belly with Meson bombs to achieve the collapse) , the node collapses, which would quite suck for any Shivan invasion. Once the opponent starts exploiting that fact, if played right, a Shivan invasion could be stopped dead in its tracks in a few jumps. And the GTVA DID exploit it when they sealed off Capella. That strikes me as a massive strategic disadvantage to the whole concept, and I think the Shivans are smart enough to figure that out in 8000 years and ditch the concept. Maybe the Ancients themselves already exploited this fact when they closed the Knossos node in Gamma Draconis. This seems quite likely, considering how fast the node stabilised once the GTVA activated the portal, meaning when the Ancients opened it, and they had it open much longer as evidenced by the fact that they had enough time to build another Knossos in the Nebula (which I think the Shivans created by blowing up the star in that system, btw), they also had a stable node they had to collapse in order to stop the influx of Shivan warships. They may have destroyed one of the Shivan's Lucifer's, which they no doubt used for their invasion, in that node after the supernova. Either way, I think there is a solid enough rationale for the Shivans to abandon cap-ship-shields.