@Flacman3000
Yus. Thank you. And sure thing. You you're looking for:
Mod Folder > Data > World > Faction > default_ship_roles.json
To alleviate your anxiety, first make a copy of it and add Z to the front of the name so that the game doesn't read it and so that it goes to the bottom of your list. If something goes horribly wrong, you can delete the original and remove the Z from this copy and everything will be ok.
Open default_ship_roles up with notpad++ and cntrl + f to search for the ship names your looking for and delete those lines- they won't show up in stores or faction fleets after that. Just make sure you don't erase any brackets and everything will be fine.
The individual .faction files can control the spawn rates more finely if you don't want to get rid of something completely, but not every ship will have an entry and you'll need to know the ID for the ship to add it, which you can usually find in default_ship_roles if it isn't already there.
I'm not sure if it's fool proof or will have problems down the road, but, so far, anything I've removed hasn't shown up in faction armies or stores. Theoretically, I think blueprints and derelicts and stuff for it will still be discoverable in game but I'm not 100% sure.