This is what I think. Volition probably intended beams to be on shivan cap ships, but didn't have the technology to render the graphics for it properly. What I think they did was rewrite history with FS2. To imply that both the shivans and the alliance simultaneouly and independantly developed beam weapons and flak guns and then equiped all their ships with them before encountering eachother again is ludicrous. What they do is have the player imagines that the shivans had beam cannons and flak guns in FS1, even though they didn't in the game. Evidence of this is in the FS2 into cutscene. The Lucifer there fires what obvioulsly is a beam cannon that we're familiar with in FS2, not a flux cannon animation typical in FS1. Now, it doesn't show any of the other ships having beam cannons, but I think they were supposed to.
What I want to do is reinsert this back into the FSport (unless it's already been done, I'm not that far into playing the port yet). I've never done modding, but I want to pick it up. Basically, I'd just leave the shivan ships as they are in their FS2 iteration, with all their beam cannons and flak guns, but the Terran and Vasudan capital ships would use conventional laser cannons. To make the Terran and Vasudan ships capable of surviving prolonged engagements with Shivan warships, I'd modify the Terran and Vasudan turrets slightly. I'd designate the turrets that in the FS2 iteration were set asaide as anti-fighter beams or flak guns as anti-fighter lasers. They'd have a faster rate of fire and better tracking abilities as conventional lasers but each bolt would do less individual damage. The turrets that in FS2 were beam cannons would be heavy anti-cap lasers. These would be slow firing, but would do tremendous damage on hit. Not nearly as much as a beam cannon, but if you got hit by one you're pretty much toast. The good thing is that these cap ship lasers wouldn't track fighters, but would only fire on capital ships. The anti-fighter lasers could and would be employed against cap ships, though. These new lasers would be like the anti-ship guns in Starlancer. I've never done a mod before, and I have very little time on my hands, so don't hold your breath. If anyone wants to help me with this (Goober, please?) that'd be awesome.
As far as the shivans ability to use unchartered nodes, well that has a lot to do with what happened in Cappella. A big clue is when Admiral Petrarch says "Perhaps the explosion of a star is a bridge between this universe and their own." In the dying moments of the star, it must of created some sort of subspace phenomena that allowed the Shivans to warp directly from where they were to some other location in the universe, or some other univers. This might be what allowed them to discover us in the first place. The go around exploding stars jumping to random locations. They send exploratory task forces into these unknown regions (the Lucifer fleet) to exterminate any life and look for new candidate stars whose explosions create powerful enough subspace phenomena so they can warp to new unchartered locations.