It certainly appears so - you may have noticed, in missions such as the first nebula patrol, that the AIs on you team will fly a little faster than you unless you allocate more engine energy
I think they do use it at least when applying afterburners a lot (e.g. when traversing large distances), since their burners recharge much faster than normal in this case; the only way you can keep up is to allocate all energy to engines.
Fix: don't do that.
nice and simple.
Anyway, I think that the biggest problem with the fighter AI is its close-range dogfight capabiltiies, or lack thereof. They are actually pretty good at long range, firing a lot of shots with extreme accuracy, but when they get near you they just run circles around you (without even afterburners, simply cruising) without making any attempt to face and attack you or run away as long as you keep them in your ship's front view. If this is changed around, maybe by having them apply a quick afterburner boost to get away and then turn around again to fire, they would become far, far more effective. Also, they don't seem to use coutermeasures a whole lot, and when they do the CMs aren't accompanied by any evasive maneuvers from the fighters at all, so they usually do not work.
On an earlier note, there does seem to be one exception to the long range combat; the computers tend to fire missiles from long distances well before the missiles are in range (don't ask me how they acquire lock), which results in them exploding before they reach their targets.
