I actually was looking at making a mod with a "PT Boat" and I think the simplest way is to add a new fighter class which I will call the "Interceptor".
If I can edit the parameters (some I know I can others I am not sure yet) it will do large damage versus scouts, refinery and trade ships and pathetically light damage versus everything else.
It can be used in a hangar at a system to interdict trade ships (and accumulate wealth as a result) and to blockade scouts on autopilot (so they can't scan core worlds for a Novalith fix later in the game or see what has changed in your system). It also would work well as a raider force with carriers on undefended enemy shipping. Of course, if they have escorts, the interceptor will be the least desirable asset to defend or attack with as it will have almost no shield or armor and less effective weapons compared to other fighting craft.
It basically fulfills the role of interdiction. Probably a good comparison of it is the WWII Mosquito bomber. Made out of wood and for speed. They were used to intercept V1 bombs, for reconniasance and blowing up trains and coastal shipping.