modifying the prirate composition has never been an issue for me since they re-did it in Diplomacy, you can specify composition of fleets, numbers even add your own cap ships and things.
You could specify the type of ships in the pirate waves and their probability of appearing.
The problem is the exact number of ships and exact composition of the raid and the exact probability couldn't be specific. You also couldn't get the fleets below twenty (maybe ten early game) as it seems to have been hard-coded in.
Everything is a multiplier and covers things like fleet logistics, resource costs, planets owned, trade vessels in play, etc. added to apparently minimum sizes for raids that couldn't be changed.
My goal had been to have pirate raids consisting of a single ship and regrettably that wasn't possible.
Based on what Lavo said above--and assuming he's correct--I'm going to try a workaround and see if I can trick out a single ship raid...if I can manage the time.
I'd love to see some experimenting and results from others on this.