In the fs1 tech description is where you find out about the lucifers flux cannonshttp://www.hard-light.net/wiki/index.php/SD_Lucifer
. I have no doubt command created they're own flux cannons from reviewing the scans of the lucifer. Otherwise i bet you in fs2 the weapons you'd be missing are beams. Plus, i bet sol could develop they're own beams since the lucy pretty much split in half via an explosion in the sol node, and the front half of the vessel is in sol probably to be salvaged and reverse engineered. Or perhaps earth got a transmission of the lucifer scans, since that mission happened much earlier to the demise of the lucifer
And also technically with the nebula thing. The shivans might not have been in the nebula from the start. Remember bosh did go and plunder ancient archeological sites, discover the knossos, and activate it. NTF ships were the first ships to enter the knossos from tv space. Bosh's objective was to find the shivans and then open relations, perhaps ntf nebula exploration ships did more than go through the nebula, they could have gone through the other knossos device to attract the shivans. I mean, bosch did have to find them first, after 8000 years you can't expect the shivans to still be at one place. This theory of course works off of an assumption of course that the shivans weren't in the nebula, this can't be proven. Something that can be proven is that the knossos did have to be activated. And since the knossos had to be activated, that proves you couldn't use that node until you flipped the on switch to the knossos. That's probably why the shivans didn't come through until bosch intervened.
What the knossos actually does could be ten fold. We do know that the knossos re-initializes dead and unstable nodes(i don't want to go so far as saying the knossos can create nodes, but i bet it can since it's one of the few luxuries the ancients had to colonizing galaxies). That's for sure, it's one of the reasons the node for that knossos still worked after the knossos was destroyed. Which breeds another question, why didn't the node with that knossos stay stable since the ancients left? Well, it was most likely an unstable node that required the use of a knossos, and over 8000 since the ancients were gone, seems more than enough time for a technically undependable node to become unstable again without the knossos being active.