For some options related to either, you'll probably be breaking some new ground.

I'll go over some details below which may help you achieve what you're after.
There is no scale factor for the thrusters, they are designed to present their effects 1:1 with the scaling of the ship they are attached to. However, you can move them or replace them to change their position and/or structural appearance. The script file option can be used for positioning, but that's largely designed for importing complete custom ship frames. Instead, you may just want to import your own custom thruster mesh that is pretty much invisible (one very small triangle for example), or some other shape you might prefer. The filename you'll want to use is 'frame-thrusters.x' and the file will need to be placed in the global \ships folder.
As for hiding their exhaust effects, that can be done with the jet2.png image file outlined in the customizing kit. You can import a blank png file or something else. However, that is a shared resource, so just be aware that you'll be altering all thruster outlet textures it is linked to, including engine and thruster nozzles for all human ships.
As for the cannon barrels, those use the filename 'frame-cannons.x' and the same global \ships folder as the thruster nozzles. The firing positions are locked into place though due to certain placement, scaling, and alignment dependencies (including multiplayer consistency). However, if you're just trying to remove them and don't mind beams/particles just appearing in front of ships (which is sounds like you wouldn't mind for the aesthetic goal), you can import a small and almost invisible mesh to replace them, or some other design you might prefer.