i think most people greatly overestimate trebs. they aren't automatic kills. they're not even particularly likely kills, except maybe against bombers (that the UEF doesn't frequently field, and almost certainly not in a fashion that would be vulnerable to a dedicated treb strike). fighters can rather easily dodge them. if there's cover (and the pilots aren't idiots), there is ZERO chance of a kill.
Trebs aren't a guaranteed kill by any means, no, but they ARE a gauranteed harassment and standoff tool. Providing fighter cover is difficult when you have to dodge staggered Treb shots at the same time. Similarly, Trebs being present all over in the battlefield means that whenever a bomber IS deployed, it's got to deal with the major threat of Treb spam.
---
As far as spam against warships, Trebs are decent, but far less effective against Federation warships than on Tev warships (especially the Capellan era ones). Still, correctly applied, you can reliably snipe one or two of a Karuna's torpedo launchers without too much trouble. Picking away at the point defenses also helps, though I think going for the engines is probably a more effective tactic (damage its tactical capabilities, and potentially strand the ship where it is--serving as a possible lure for other warships, etc.).
Also, remember that an increasing number of UEF pilots are fresh meat--so the Trebuchet would probably do better than you might think as an anti-fighter weapon.
Honestly, in most circumstances I'd think a couple wings of Artemis bombers would be much more threatening when armed with tons of Trebuchets rather than Cyclops. Reasoning being that it provides consistent anti-subsystem capability, stretches enemy fighter cover very thinly (five kilometers in any direction, simultaneously...), and deals more reliable (if less overall) hull damage over time. Trebs can also be dumbfired up close, in the odd circumstance where that'd be useful over normal firing from kilometers away.