This idea has been used in many mods over the years.
The idea of using PDC's as seperated weapons is a logical alternative to just having PDC's. PDC's are very powerful and will decimate fighter groups, drones, and such so many modders have taken the steps to seperate them.
The thing is, you have to mod so that the AI will use on its designs. You will have to change weapon family numbers, add the ability to the Design creation files, or use AI Tages.
Getting the AI to use your weapons is an effort of trial and error.
I suggest reading or posting over at
www.spaceempires.net forums in the Mod Works section and asking some questions there as well as here.