Those hullmods will be on regardless of story points. For example, Expanded Missile Racks will go on a ship that relies on missiles, and the less important stuff are luxuries that get cut out. All that means is that more max OP is the same, instead of varying by how expensive the integrated mod is.
I feel like this is the correct point.
In my view, s-mod diversity doesn't matter so much as the final ship build diversity does. That actually leads to different experiences in game. As far as I can tell, s-mod diversity just means less free OP to spend than we have in RC12. Any version of the mechanic, played "optimally", is going to end like this I think. What is the maximum amount of stuff that I actually want that I can cram into the ship.
Now, it may be we want to reduce the amount of free OP for ships (looking at you safety overrides), but that's a question of overall power as opposed to diversity (which is what I interpret "interesting usage" as).
As it is, I'm already using s-mods for hull mods you didn't list. But maybe I'm just strange. I've s-moded Efficiency Overhaul and Surveying Equipment on a set of 3 Revenants, and then slapped on Auxilliary tanks and Expanded Cargo holds as well. In another run, I've got 6 Revenants with s-moded Surveying equipment. Simply because those the hull mods one typically puts on logistics ships. So assuming you're investing s-mods into logistic ships, then I see reason to use a different list of hull mods.
As for combat ship hull mods, I'm willing to bet the 90% most common hull mods come from a list of 14 or less - and thus we've already got ~50% hull mod diversity (your list of 6 + hardened subsystems). You'd simply be pushing it to the other 7 or so other common combat hull mods. I feel like the screen shot listing hull mods is very misleading in terms of "viable" hull mods. I don't care if I can make it free, I'm not going to throw Additional Berthing or Surveying Equipment on a combat ship. A number are straight up not possible (Militarized Subsystem, Makeshift shield generator, Escort Package, Assault Package, Converted Fighter bay) on typical combat ships either.
As an example, if I want my Paragon to have Hardened Shields, Stabilized Shields, Heavy Armor, Auxiliary Thrusters, Integrated Point Defense, and you tell me Hardened Shields and Heavy Armor are no go, I'll just apply it to two of the others. Build is still the same, I'm just short 25 OP when comparing builds. Guess I have 25 less capacitors on that particular Paragon. Ship flies basically the same either way.
If you really cut down on the value of the OP saved per story point, I think the it is possible that less common hull mods are less likely to show up on ships at all, not more, since overall OP will be tighter, and so you ensure you have the critical needs first.