Starsector 0.97a is out! (02/02/24); New blog post: Simulator Enhancements (03/13/24)
Yeah, that's the intended behavior. If you don't want the missiles to render, either set this render hint:RENDER_LOADED_MISSILES_UNLESS_HIDDENOr do not set the RENDER_LOADED_MISSILES hint on the weapon.I know that doesn't help if you want HIDDEN to fully hide vanilla missiles, but that's the only way to go if you really want that behavior. Also, some fighters (i.e. Dagger, Thunder) rely on this behavior to render properly.
Wyvern is 100% correct about the math.