Don't forget about the theory that said beams were communication and the Sathanas was a keg of beer!!
Anyways...
The Flak makes sense, though we definately stole beam tech from them... the Shivans would be able to scan, from in subspace, our ships. Why do you think they're all so superior to ours? they probably know every design that has ever entered subspace, including complete specs, full-detail tech diagrams, etc. From the first ship we put flak on, they probably had the design... they would likely test it out a bit; find out how lethal it is. They find it's effective and decide to use it!
Why waste the big firepower? Would the GTVA send in the Colossus against a wing of fighters? I think not!