Actually whats probably knocking your weapons ofline is the thermonic torpedoes, they spam you with them, (i've never seen them use subsystem targeting btw), they each have a chance to drain 25 power from weapons and engines. The Detructible ones are a garunteed -75.
As for tet procs. the base is somwhere around 400 for us. Most NPC's get significant modifiers to weapons damage. 5K sounds like somthing a bit more, but still it would explain a lot.
They use subsystem targeting on weapons constantly.i was debuff hawking trying to figure out how to negate it, and it's a beam target subsystem.
If you want to farm Romulan Marks via space missions, they're unavoidable. They aren't difficult (even my Eng Excelsior chews through them), just nuisances. All the subsystem targeting garbage just postpones their demise and maybe throws off your alpha strike. Plus in Azure Nebula Rescue, waiting on that reboot costs you time and thus marks, meaning you have the run it yet again. Its like they know they can't beat you, so they're going to annoy you into submission. Not an entertaining fight.
My Lethean's using an all Plasma (Torps and Arrays along with EWP III) Bortasqu build. It's actually pretty effective though I'll mention I'm using two copies of Torp Spread and one Tac Team I for Tactical options.
Also something that works really, really well against the Tholians is Reverse Shield Polarity. I had two copies on this character's build for some reason and have found it to be an extremely effective way of preserving/boosting my shield strength against their Tetryon beams.