Well i think these effects should scale down (get smaller) as you get closer to the action - maybe x4000 can tune it.
You are perfectly right - the shot effects are very large compared to the explosions and ships which looks really odd - this was done to make them visible in "zoomed out" view but as it is now its less than optimal.
I don't really know what happened with the scaling effects and icons feature, that was a fairly major suggestion way back
Actually, i have an idea how to make the shots look much better.. (less opaque) .. suggestion with graphics is coming up
x4000 sadly i am not 100% sure my suggestion i posted concerning this is really better... Atm some shots look awesome (double lazers) in both far and close but energy bombs look nearly opaque from afar (circles indeed) - i think i am not much of a help here ;p