As for me its another unnecessary nerf, like Phase speed slowdown nerf, first of all, the decision cost means bad isn't best one, because some hullmods are already situational enough, like Heavy Armor which reduces maneuverability, or EMR which only benefit missile focused ships, so they aren't built in always already, its just nerf of ships which rely on armor or missiles, and make hullmod which supposed to just improve ship actually harm it looks strange, it is basically turning smods into dmods, and its quite logical what people will build most expensive hullmod from their loadout, if you have 1 sp which can apply any hullmod, its logical to built most costly one. Game have other more important problems, and smodding expensive hullmods is not one of them.
And if you don't like the fact what 10 Op and 40 Sp hullmods cost same 1 SP, I think there more ways to resolve that without complicating balance even more, like make expensive hullmods cost several SP points, or just give fixed OP count per spent SP on ship, or just leave as it is now. Story points have issue that you can gain much different benefit from spending 1 sp in term of usefulness, ranging from useless options, such as most quest options, like get little more reward in quest, or not raid objective in raiding quest, and receive twice less amount of money, considering that these quests don't give much reward, or use same point on built in hullmod, so reward ranging from gain insignificant reward to permanent benefit, but again, root of the problem is not that built in option is too good, is what that other options are too useless even to consider.
Also another issue I think, its also indirect nerfs ships with built-in mods, since they won't receive s-mod bonuses, like Apogee won't have bonus from Sensors hullmod, and non-science ship with built in will have it, to be honest this feature shift balance too much.