I'm actually rather impressed with your theory; that's some pretty good out-of-the-box style thinking. You managed to explain why the Shivans are cold and hostile, why they aren't interested in planets, the significance of nebulae and Shivan 'comm nodes', and the endgame events. I also like how this contrasts the commonly used theory that argues that the Shivans have a divine purpose of cleansing the universe of dangerously expanding civilizations like ourselves and the Ancients. Maybe the Shivans aren't so special afterall -- they're just a spacefaring race like ourselves but with a more unfortunate history.
Anyways, my first question was "Why go through all the trouble of nuking a star to make a new nebula when there's plenty of them around already -- a fact that Freespace's beautiful backgrounds reminds us repeatedly?" But then I realized, maybe only certain kinds of nebulae are useful for the Shivans. A young supernova remnant would probably be more dense than a typical nebula, and also richer in heavier elements. Certainly you can't make big spaceships without a good source of heavy elements.
Another possible answer to that question would be that maybe most nebulae aren't easy to reach, even with subspace travel. Natural subspace nodes seem to preferentially connect to stars, not nebulae.
There is one statement I disagree with though:
A faction of these space faring Shivans decide to forgo terrestrial means of resource acquisition and develop ways to harvest materials from the nebulae that were present in their home system. The devices seen in "Into the Lions Den" are an advanced example of these material collectors. The briefing states you are heading deeper into the nebula but when you get there no nebula gas is present.
The Knossos portal that led you to the Lion's Den mission is certainly deep within the nebula, but why should we be led to believe that the other side of the portal is (was) within the nebula as well? We already know from the first nebula mission that the first Knossos portal took us a very
great distance. The briefing even states that "we have gone farther than any Terrans in the history of space travel". I have a very difficult time believing that the second portal wouldn't take us a similarly great distance.
Another difficulty is that all of the nebula missions display a single star in the background, while the Lion's Den mission takes place in a binary system. It also has little in the way of background nebulae. I'd expect to see at least a great wall of fuzziness in some direction if that system was once part of the greater nebula.