This whole thread makes sense in the BP universe.
Certainly Shivans and Vishnans have an ongoing agenda. And it's all about balance. That's why they're referenced as "counterparts".
You can look at this a different way, however:
The Vishnans and Shivans are conterparts same as Ubuntu and Fedayeen. They keep a balance and ruthless destroyers are needed to preserve a society of pacifists. One can not exist with the other. Clearly, it makes sense, now. The Vishnans order culls to species which pose as a thread to their own society. This may make them the "baddies", after all. Their role in Ubuntu was their last try to shape humanity, to integrate them, rather than destroying them. After all, they are great preservers.
However, about the SSI and actual canon information on that, here's a little paragraph from the FreeSpace retail box:
"In the introduction (back side), the last paragraph says: "Your nemesis has arrived... and they are wondering what happened to their scouting party." This most likely refers to the Shivan force that attacked in 2335 (FS1). "
Found here:
http://www.hard-light.net/wiki/index.php/FreeSpace_TriviaCanon teaches us that the lucifer fleet acted like a hive-mind. As soon as the lucifer had been destroyed all elements of the remaining Shivan fleet swarmed around headless.
Assuming the lucifer fleet was nothing than a scouting party which probably is deployed for years before it returns it makes sense that it took years for the Shivans to recognize that their scout went missing. The shivan race is very old, far more than 8000 years. They maybe think in different concepts of time, 32 years can be nothing for them. The sathanas fleet poses as an actual strike force of that race and the activation of the Knossos provided a new entry point for them into terran-vasudan space. The nebula beyond the portal could be remains of another shivan induced supernova 8000 years ago.
And this is where we leave actual canon information as it is on the wiki:
I don't remember where, but I did read some statements of Volition, years ago. How FreeSpace 3 could've developed. I will try to find them when I have time, but I'm afraid they are purged off the interwebz.
what they said is the following:
They weren't done with the entire story and most secrets were kept for the final Act as in FS3. The destruction of Capella wasn't just a vicious act to eliminate every terran and vasudan in that system. Most of the juggernaut fleet jumped out shortly before the star turns to ashes. They probably returned home.
The final cutscene on FS2 gives us some hints on that. "Maybe, they're exiles just like we are. Nomads wandering the universe, searching for a way back home." Look at that, we're back to actual canon information! One of the last statements was, that FreeSpace 3 would state the final war between Terrans, Vasudans and Shivans including the shivan homeworlds. Information on why the Shivans destroy everything was not given away. But tech room descriptions from FS1 and FS2 give us a little hint. You can read that Shivans developed in an environment without gravity. They are cyborgs and it rather seems as if this species had been "designed" rather than developed naturally. Probably as a weapon which, in the end, turned against it's creators. You can read this in the tech-room, it's all there.
It is obvious that BP states in a totally alternative storyline, here. Where the Shivans are rather made of "universal knowledge, being capable to adapt to any enemy, any weapon system, possible, sleeping below the waves of the universe since the beginning." Maybe, the Vishnans and Shivans were one race, once, same as Ubuntu and the Fedayeen.