Here's my take.
Let's assume that the Shivan function similarly to a hive mind, but is still capable of independent thought.
The Lucifier, would be the queen vessel. ALL Shivan ships, including the massive fleets of Sathani obey the Lucifier. In an effort to preserve energy, Shivan vessels are ordered by the Lucifier to disable beam weapons. Afterall, they have been drifting in space and if we treat them as living creatures, they would have an interest in saving their energy. As the queen vessel, this also explains why it is the only ship in existance and that we never see another Lucifier.
After the destruction of the Lucifier, Shivan forces became disorganized. This is the shock phrase. However, Shivan forces across the entire universe have know awoken from the lost of their queen. Energy weapons are reenabled, more advance vessels are awakened from strikecraft to the Sathanas; the Shivan forces begin to actually mobilize.
Now, in FS2, it's agreeable that the Shivans did not perceive the GTVA as a threat. Whereas it would be in the interest of the Lucifier to destroy any possible threats to its existance, the Shivans in FS2 had no queen to protect. Shivan forces probably then reorganized into smaller fleets (small relative to the entire Shivan species).
This is where my theory splits off. Theory A: Shivan forces are mobilizing to kill other Shivan fleets, essentially a civil war. The GTVA is too insignificant and only survives because the Shivan's best interest is removing the next greatest threat, which is no longer the GTVA, but the other Shivan cliques. Theory B: Shivan forces are desperately trying to rebuild the Lucifier. The Sathani fleet is essentially harvesting stars for raw material and making the jump back to the spawning pool of the new Lucifier. Losing a few Sathani is nothing when compared to reestablishing the hive queen. Theory C: Something is disturbing the spawning pool of the new Lucifier. The Sathani are on a direct route back. This theory attempt to explain the present of the Shivan Comm node. I think it's pretty clear that there's something going on with Shivan communication. Theory D: This is really radical, but perhaps the Shivan are not capable of reproducing intelligent life. So they capture someone like Bosch and intend to somehow change him into the Lucifier. Or maybe, the Lucifier was created by the Shivan's creator, but the Shivans themselves, are not capable of recreating it. So they need Bosch's assistance in this.