Look at it this way.
Beams have limitless ammunition. Its energy after all, drawn from the ship's reactor. This also frees space normally devoted to carry ammo, and eliminates the risk of an ammo explosion. Imagine if a Hecate carrying Helios in the millions suffered an ammo explosion.
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.
By contrast, launching a Helios to combat worthy speeds would require a torpedo tube, energy to propel the Helios, a feed mechanism. And there is no guarantee of a hit. The Helios can easily be intercepted by flak, CIWS or interceptors, even if you get it up to combat speeds. Although there is something to be said of packing 20 Helios bombs into a single torpedo that splits at a certain distance, so there are that many more projectiles to hunt down. And even then a hit is not guaranteed.
Psychologically, a beam is much scarier. Its bright, deadly, fast, accurate and very much unstoppable. In short, its intimidating. I doubt you would dare to face down a charging beam weapon. The Helios is slow, small, nearly insignificant and very stoppable. Interceptors were designed with hunting bombs in mind, and they excel at this. But there, as far as the FS2 universe is concerned, no counter to beams short of running like hell.
Cost wise, beams are cheaper. You merely pay for the beam system. Done. For bombs, you pay for the delivery system and the bomb itself. As it stands, bombers make far better delivery systems then any you can find in FS2. Bombers are capable of delivering the bomb right in the target's face, and can even defend themselves to an extent.
Pound for pound, bombs DO deal more damage. But, beams can deliver more damage simply because they cannot be stopped, while bombs can.
... If you ask me, the GTVA should design small, maneuverable ships which have a single LGreen and no CIWS, and simply escort them with fighters. Costwise they'll definitely be cheaper than destroyers, and have more potential for damage.
By the way, did anybody actually make a capital class missile/torpedo that hits like a helios but moves like a interceptor ?