Another suggestion is that fitted modules should be displayed on the ship. Like turrets, launchers(?), gasminers and tractorbeams all have models displaying themselves on the ship. Today's ships and planes have all kinds of pods/radar dishes/guns/electronic warfare packages sticking out giving you "some" idea on what the capabilities are or their setup (on fighter planes at least)

Sensor boosters could have small radar dish turning (like scorp has allready)
Repair modules could have "nanite nodes" on the ship
cap booster could have some sort of lightning rod like system that plunges into the hull (reversed warp core ejection)
sensor strength could have sensor "pods" on the hull
etc, etc.

All these things could be animated when the modules themselves are activated, making it even more clear when something happens or when somebody activates a module (in stead of some sound and a colour wash over your ship)

It would also differentiate different ships from each other, making ships even more indiviual. It would also make clear on looking at some ships what modules he does not have fitted. (good for FC's and yelling)

Special modules (i.e. navy, serpentis) would have a more awesome look/activation then others.

Then as a final addition, fake modules could be introduced so people could think they know your setup...