I think your running out of.... um.... things..
I think sins has a limited number of...... "things" "stuff that can happen"
I had this issue when I made a ship that have 5 weapon system with 50+ turret points, I had them burst firing missiles in groups of 6, and then the other end I had them detonate as nukes, all with 3 sounds for launching sounds for detonation and sounds in flight, it looked amazing but 3-4 of these ships in combat and suddenly things stop shooting, this just face each other.
I assume the game has a limit of say 65,025 things that can happen, and this would include, My missile trails, FX on shooting, and detonation, sounds, trails generated etc.
I also had the same issue when I was burst firing a Beam laser 20x 0.3 burst with Animations on the turret and impact, and with a chaining beam that split to 3 other targets on impact.
Can you do a flat damage increase without changing any of the rates of fire etc? Or is simply changing the damage and nothing else causing issues?
you can also check your Mesh in developer use "CTRL shift ." to bring it up then "c" entinity info and "Q" weapon states, to see if your ship has the correct points for shooting.