Choices that come at a price make them more meaningful in my experience. Currently, weapon choice itself has a fair amount of importance. Generally every weapon has a weakness to it, and you offset that weakness by playing to the strengths of your weapon/ship.
The whole idea of having weapon mods would be to even further specialize. I feel that since you already do so much to emphasize the strengths of your load out doing anything to strengthen it further should have a more pronounced cost or else balance would be very hard to maintain.
As it is, the enemy has trouble doing anything to my fleet with 5 or 6 Tempests loaded with 2 pulse lasers, integrated targeting, and enhanced engines. Rest goes into flux vents if I recall. Imagine the madness if I could improve their range, turret speed, and damage at no penalty.