Yea, the missile bays are the problem. The directed energy weapons are fine. I think the missile bays are actually kind of interesting though because they allow you to get an enormous volume of fire into space really quickly. To get 24 missiles into space using turrets, you need 8 hardpoints, instead of just one. Yes, you are only using 8 tons versus 100 tons, but tonnage tends to not be the limiting factor as much as hardpoints on large ships.
Consider a 10,000 cruisery thing. It has 100 hardpoints. It can have 10 bays times its power plant rating (probably 30-40). Let's say I use all 100 for triple missile turrets. Going with the 80% bearing hull, that's 80 turrets, or 240 missiles per barrage. Not bad, but I have no point defense.
Now let's try missile bays, both 50 dton and 100 dton. I'm going to assume a max of 40 bays. That leaves 60 hardpoints, so we know right away that we can put an extra 60 triple missile turrets. 80% of 60 is 48, and 48 *3= 144 missiles. If I have the tonnage, I'll put 40 100dton missile bays. That's 4,000 tons, and is probably excessive unless this thing is a flying missile battery. Still, those 40 missile bays allow me to fire 40*80%*24 missiles = 768 missiles. Whoa. Let's not be quite so insane and use 50 dton bays--that's 2,000 tons and it comes out to 384 missiles. So either way, we're getting MUCH larger missile barrages with bay weapons when hardpoints are a limiting factor (and I do believe strongly that hardpoints are always the limiting factor over raw tonnage).
And the above were just silly designs that had no point defense. Once you incorporate in the need to spend a bunch of turrets on point defense, it becomes quickly obvious that missile bays are hugely awesome for missile combat. That might go a long away alone to help soothe their relative weakness in terms of individual weapon damage.