Having one s-mod come from credits, one from story points, and the third one unlocked via skills seems like a potentially interesting way to diversify the cost without trivializing it. I still think there needs to be a cost more than credits, though. Credits scale to near infinity in the late game so there's no credit cost that makes sense both in early and late game. But since story points seem, to me anyway, like a token for time played, adding a time component to the credit cost might help balance it out.
Like, you want to put your ship in for a permanent hullmod, you have to store it at a place where the work can be done (either paying that storage fee or paying the cost of building up a colony to store it for free), and then leave it there for some amount of time (maybe something like 2 days per ordinance point, times a multiplier for ship size so that s-modding little ships can be relatively cheap but s-modding big ships really hits the ol' bank account) while the mod gets built in. That would be a cost significant enough in time and credits to be felt, but not enough to cripple a players ability to field their fleet.
