All beam weapons except for meson beams are affected by atmosphere.
Damage of those weapons is reduced by an amount depending on density of the atmosphere.
I do belive it goes something like Damage Reduction = atmospheric pressure x 100 in percent. Damage is rounded down.
This means, a pressure of 0.2 will reduce damage by 20%.
Weapons (such as gauss cannons) that will deal only 1 pt of damage are totally ineffective on any kind of atmosphere, due to the round down.
At a pressure of 1.0 or more, all beam weapons except meson beams become ineffective.
Note: I am not sure the formula is correct, but I _am_ sure, that atmosphere of 1+ renders all beams useless.
Note 2: CIWS work for PDCs, and given they are basicly a Phalanx system on steroids, I don´t see, why they shouldn´t. (Yes, they use gauss cannons, but they are very short ranged, so the atmosphere has not enough time to effect the shots)