The only way I know is to:
1) Build a ship skeleton.
2) Build the "modules" you want to swap onto the skeleton.
3) Make the module meshes particle effects.
4) Create Conditions where the particle effects are called.
From there you will need some way to do a buff where damage is the condition.
I don't know how linear you could make it. One thing I am toying with is giving factories the ability to spawn other factories and have a separate factory for each capital ship (yeah--I know).
The factory could give a buff to the units it produces which could be your damage conditions.
Somebody who is a genius will have to take it from there.
Maybe working with the unused passive slot this might be made to work as well.
Sounds like a psychoak-volt-zombie-goa project.