In retail, the AI cannot use trebs at all IIRC, because of some conflicting table targeting priorities which prevents them from EVER being launched without the mission designer specifically scripting them to be used:
"Despite being one of the most effective anti-bomber/anti-turret weapons in the game, the AI is incapable of firing the Trebuchet. This is because of the combination of the "bomber+" flag and the "huge" flag in the table files. The first restricts the AI to firing the missile only at bombs and bombers, while the second prevents the AI from using it against smaller ships. Since these two types of targets are mutually exclusive, there are no valid targets at which the AI can fire the Trebuchet at. If you wish for AI to use Trebuchets in a mission, use the good-secondary-time SEXP."
This can easily be changed by simply editing the tables or just scripting missions properly so the AI can use them.
The AI (fury AI or not), is incapable of properly avoiding trebuchets at long range, whereas a human player can avoid them quite easily as long as they know the "trick" to doing so and aren't otherwise occupied by say, a swarm of angry fighters on their tail. I find this "imbalance" to be much more of an issue because it's not so easily fixed - the AI will almost always be vulnerable to trebuchet-like missiles because it just doesn't know how to properly evade it, and won't unless someone programs the AI with the proper evasive maneuvers to evade trebs, but then that'd open another whole can of worms in making the AI considerbaly harder to kill with missiles, perhaps to the point of aspect seekers being useless...
I find this "imbalance" the major issue with Trebs, and not how they can harass capital ships with impunity due to outranging them. I don't find that to be a problem at all, seeing as anti-fighter beams are basically pure RNG whether they hit or miss you and completely bypass your shields, outranging them is the only real "skill-based" counterplay, so I think Trebs are fine in their interaction with capital ships and have a very necessary place if the player is ever instructed to engage AAA-beam armed capital ships.
Plus, it's very easy to fix in a mod, between the aforementioned armor.tbl and bomb flags, capital ships just mounting treb-equivalents in return. There are also other ways such as just giving capital ships shields, which may work depending on your setting.