It is possible to change s-mods, but it involves double respec and losing third s-mods for all ships. For me who took no Leadership, that costs me two story points, once to respec into BotB to get third hullmod and another to respec build into my Combat/Tech/Industry build to remove the third unwanted s-mod from Zigggurat. Of course, just about every build I see posted has a Leadership capstone, usually BotB, and respeccing out of BotB will cause so many third s-mods to disappear from everything, and ships not in the fleet do not get to choose which s-mods get dropped.
I would like an easier way to change s-mods because respeccing twice is annoying hoop-jumping.