Beams deal more damage relative to their size. A beam turret consists, at most, of a firing mechanism, power supply ( the reactor ), amplifying beams and targeting systems. They also guarantee a hit. Nothing stops a beam save a shield, and no capital ship in FS2 has one. 'Cept the Lucifer. And they can be overcharge to deal more damage.
Since when did shields do anything to stop beams? The AAAfs seem to chew through my fighter just fine with full shields.
I'd assume that they'd go straight through the Lucifer's shield system as well. Helios on the other hand, can explode point blank and my fighter isn't even scratched. Anti-warship torpedos do nothing against shields, which is why they couldn't just bomb out the Lucifer in realspace or even disarm its cannons.
Yes, that may be purely conjecture, however, that is the behavior that is exhibitied if you give the Lucifer "surface shields".
Tempests do more damage than Helios on shields.