Programs like Gimp (which is free) can be used to splice current sprites into modular bits, which is what most people who design new ships (who want to mimic the art style) do. The ship editor takes care of the difficult (from a coding perspective) part of assigning the positions of turrets, engines, hitboxes, the shield radius, center of mass, etc, and creating the .ship file needed. Its main purpose is definitely not editing current ships, but for making the creation of new ships more accessible.
Something like a modular editor in game to customize ships is unlikely to happen, from what I've heard. Modding fills that need already, for the most part, and creating and integrating something like that into the game would be an unnecessary challenge.
