when you've researched higher engine technologies, civilian shipping lines will build new designs of ships with the higher engine technologies. They will also scrap their oldest ships and replace them with newer ones. I'm not too sure on how they decide on when to retire old designs.
Design? yes. Modify? not to my knowledge. Customize? not to my knowledge. Upgrade? not to my knowledge. Refit? not to my knowledge. Change? not to my knowledge. Retire? maybe.
do civilians design or modify their own ships? Can they customize their ships in any way? Can they upgrade them, refit them, change them, or retire ships that are already working?