A Galaxy class attempts to fire it's two proton cannons once every 4 seconds. However, it appears to be unable to fire while also firing a torpedo volley, which takes a bit less than 4 seconds to complete. The torpedo volley is on a 10 second cycle, which because of the inability to use both weapons at the same time, forces every second round from the proton cannons to be delayed by 2 seconds. This causes it to fire after 4 seconds, then after 6 seconds, then after 4 seconds, repeating. DPS is reduced by approximately 20%, to 360 instead of 450. The cycling of the individual barrels on the proton cannons does not seem relevant.
To view for yourself, simply watch the game timer while a Galaxy shoots at a naval target in torpedo range, then watch it again while shooting at a land target without having any torpedo targets nearby.
Fix: Without getting into a balance discussion, I would just shift the torpedoes to something like 2 every 4 seconds @ 100 damage each, raising their dps from 20 to 50 and at least making them slightly useful. This would only have the potential to delay the proton cannons once on the initial firing, vice continuously for every second shot. As it currently sits, Galaxy has just over half the torpedo dps of a t1 sub...
Edit: Grammar.