I dont think there is necessarily a problem with a small number of the most expensive hull mods always being the ones that get s-modded in and of itself. The main worry is that this system will affect overall balance decisions, as the OP pointed out.
If the game balance is totally blind to the existence of s-mods, such that ships and mods are balanced as they always had been based around op cost, then thats one thing. But if you start to see balance decisions, nerfs to some ships because its assumed they will always have these free high op hull mods in player hands, nerfs to some mods because they will just always be s-modded and so the assumption is they are 'free', etc, then the whole system needs a rework because the entire spirit of the story point system was kind of like its a special player power above and beyond what is normal within the universe, and the builds and balancing and everything should work with out a single s-mod being employed.
Currently s-mods being the only way to invest in a ship with story points to make it special might contribute to the sense of a dilemma where there isn't any. If there were other ways they could be spent to improve a ship and free hull mods was just one of them, and there was say some kind of maximum investment you can put into a single ship, then the return of a sense of options comes with out the need to try and make the s-mod system do everything for you in terms of special customization.
The romanticized idea is to see them as 'install a special hull mod to make the ship unique'. This places in the mind that the specific hull mod is somehow special to that ship, as if some justification or backstory might need to exist to explain what makes this ship so unique. If however it was as straight up as 'the most expensive hull mod is free', which is what it essentially is, it sounds less like you did something personal to the ship and so is less satisfying. By adding alternate uses of story points on ships, it can return the unique sense with out disrupting the current workings of the mechanic itself.