Ghostavo, what problem do you see with jamming Shivan communications? I think it's a reasonable tactic, though if somehow it isn't then Pegasus stealth fighters + Stillettos (or Trebuchets, SOC probably had access to those way before the player does) could disable the comms and engines of a warship so Shivans can't call for assistance, while Erinyes wings take out Shivan fighter cover. Board Shivan vessel with an Argo (that's at least several hundred troops, if not thousands), plenty of firepower (remember SOC gets access to special/non-standard weaponry) and numbers to capture a corvette, let alone a cruiser like a Lilith.
As for beams not being bigger versions of each other, I'd somewhat disagree. SRed, LRed and BFRed are all the same energy type, thus the same colour (my guess is it's a laser), just each version has more energy inputted for the discharge.
SGreen, BGreen and BFGreen/LRBGreen are the same energy type too (plasma?), and this you can prove for certain since all the TerSlash and BGreens of the Colossus become LRBGreens when they overdrive the beam + reactors.
Vasudan beams are photon in nature, I believe they say so during the end of 'Surrender, Belisarius', which is why they have a yellow/golden colour. SVas, VSlash and BVas are just different configurations of that energy type.
32 years is plenty of time to research better weapons to kill Shivans, I mean in Hall Fight those chain/gatling guns brought down 1 of the Shivans (I'm pretty sure no one thought Shivans were going to be that big & cybernetic), and in the zero-G of space, a soldier should be able to carry around mini-Subachs/mini-Kaysers (though there may still be the issue of inertia...)
No Shivan armada's coming to save that warship SOC hauls off if that warship (or its dead fighter guards) can't send out that call for help, now can it?