You're all forgetting that most of the weapons in-game would use antimatter as the source of their destructive force
um... no? honestly, abilities use anti-matter primarily as a lore-friendly way of explaining why you cant fire your Gauss round, or use seige planet, or phase missile swarm whatever every 10 seconds, as well as creating a way to prevent ships using abilities or enabling them to use abilities for longer (i.e. AM stealing abilities, Magnetic Clouds and Suns/AM improving/increasing abilities respectively)
i mean, lets say you have a fleet in a magnetic cloud UNGW, each ship can still fire its standard weapons, but all abilities are disabled. this means that anti-matter is not used in any weapons in the game. it may be used to power the ship and engines, and, ultimately, may be the thing provides the power for the auto-cannons and lasers and missile loading systems etc, but that does not tranlate into increased firepower. its like a nuclear powered ship or submarine is no more powerful than one that is run on diesel fuel and electric batteries... (except the nuclear powered ship/sub can do a kamikaze run but...)
also, even if it was used, the only weapons that would be improved by utilising an anti-matter reaction would be missiles (i.e. just like a nuclear explosion, plus propagation effects). lasers MIGHT get a higher damage output, but i dont believe a matter/anti-matter reaction can generate a laser itself, so the power it does create still has to be channeled through a laser capacitor and so on and so forth. and im sure beam weapons, autocannons, plasma cannons, wave cannons, etc etc wont be affected by utilising an anti-matter reaction because it simply doesnt apply.
im not sure if you know how a nuclear reactor works, so if you dont, ill go through it briefly:
a nuclear reactor uses a controlled nuclear reaction to create heat (so, you fire a particle at an atom, that atom shatters and fires more particles at other atoms, creating a chain-reaction. this is controlled using a dense metal like lead so that the reaction stays within manageble levels). that heat is used to heat water until it becomes steam, which then runs through a pipe at high speeds (due to pressure) and turns a turbine (like a big windmill) which is what actually generates the electricity. the steam then runs through more pipes, eventually cooling back to water, cooling the entire system, before going back to the reactor to be heated up again and thats a nuclear reaction. it also happens to work exactly the same as a coal-burning, fuel-burning and gas-burning electricity generator, except the potential for power generation is much greater.
so, point is, a matter/anti-matter reaction is very similar, the matter comes into contact with the anti-matter, they cancel each other out and create massive amounts of energy, most commonly heat, light and radiation, follwed by some less common/useful types. so, the fact of the matter is that an anti-matter reaction has nothing to do with how much damage a laser does, aside from the amount of power there is available to channel into the weapon. just powering a laser with M/AM generated electircity does not give it the characteristics of the method in which it was generated...
the only thing i can think of is if you could create and channel anti-matter particles into a beam and fire them at a target, creating a M/AM reaction between the weapon and the target hull... however, assuming sheilds in Sins use super charged ions and protons or something similar to create the shield, i cant say how effective this weapon would be against shields... possibly entirely ineffective...
so, long story short... the only existing weapons that would be benefitted by using a M/AM reaction would be missiles, and possibly a new anti-matter beam weapon, though its effectiveness versus shields is suspect... everything else is simply inapplicable