Ok, I'm gonna throw some conspiracy theories around.
1. Why did the shivans send in one superdestroyer when they had hundreds of juggernauts.
And interesting fact, if you notice, the Luci had 6 reactors and the explosion took out the SOL jump node. Then if I am remembering right, it took 6 meson bombs to destroy the nodes in FS2. And that brings the question, is it just luck that the Luic had just enough explosive punch to destroy the jump node? And that brings up another question, was it luck the luci blew up at the right place to destroy the jump node, or did it self-destruct?
no mension of self destructive purpose, the shivans went into battle regardless of how strong the GTA or PVN was, not an opportune time as many people suggest as the shivans are xenophobic, war is thier only means witch means they could head into any territory no matter how strong, and as you say hundreds of sj's, they would bear down on the enemy and squish it no matter how heavily reinforced they were, Tombaugh station is just an example and the destruction of Vasuda and almost earth. witch confirms they saw them and crushed them.
2. Can the Knossos lock nodes instead of just opening them?
If you look at the Knossos, you can see what looks to be tech of the ancients. Could this have been a last ditch effort to stop the shivans by closing down jump nodes. And if so, could shivans open them? How many Knossos are there.
im pretty sure there are a few around.
the shivans could not open them, my guess is the ancients closed the knossos, that left a few destroyers a few cruisers and a lucifer behind with

of bombers and fighters in epsilon pegasi or capella or even gamma draconis, meanwhile some place like Mirfax there are freighters and other ships like that.
3. Can Knossos cloak?
In FS2 it says that they did not detect the Knossos before the were turned on. Could that mean the cloak when inactive? Is this why the Knossos could be found in Ross128? Could this be while GTI had such an interest in this place?
trying to cloak a station of that magnitude would be absoutly enormous, not to forget the energy of the interlocking arms and trying to cloak that just wont work.
yes it was deactive, so it appeared there was nothing out there.
and a knossos in 128? i dont think so i think the lucifer was ready to attack the GTA after the shivans got trapped by the Ancients thousands of years earlier.
4. How did Bosch know the location of the Knossos and how to flip the on switch, and how did they build ETAK.
An interesting thought, did the shivans pick him out, tell him the plans for ETAK, where the Knossos was? Could they have been using him to open it and give them the knowledge to open it?
1st off the shivans are xenophobic, secondly they speak in em pulses. its highly unlikey bosch knew he got picked, like saying portugese to a japanese man, wouldnt of understood, i can only imagine that the the old GTI Rebellion had some research somewhere on such a machine, and it only took bosch to find it and complete it.
5. Capella supernova
No ones knows what they did, but it is an interesting thought that it could ahve been just a distraction to end the war.
only

knows the answer to that, some speculate on a massive jump gate to thier homeworld, others speculate that it was to cut the shivans off from the GTVA, some others say it was a warning to the GTVA from the shivans.