You say further down that you're not serious, but I actually agree with you, as a lot of SEs are magical. I'd be happy if SEs were erased, if some of the more "logical" ones would automatically be applied to certain weapons. Forced shell effects on all cannons, for example, because when a boat gets hit by a big shell, you bet grandma's bonnet it gets knocked around! Beam lasers should automatically cause heat on the target to rise, because you are cooking them with a laser, LOL. Perhaps all burst could have a bit of shield 'bleed through' due to their fast speed. All rail guns could be superpen, because I would just assume they would be anyway. Etc.
As for MCs, cannons, and other ammo-based weapons, have it so you buy specific ammo types, like you do for REAL GUNS (corrosive bullets, incendiary, etc). Ditch the OP rounds like emissive. No engineering required, and it offers more flexibility!
Long story short, I think you are on to something, but sadly Frontier will never actually do this.