i mean you are just calling into question why the 2-logistics limit even *exists* now if the s-mods entirely break it. The whole point was to stop people slamming every logistics mod on their civilian ships and now we're right back to it. S-mods! So you don't have to make choices.
It's a choice between putting an s-mod on a logistics ship or using it elsewhere, though. Augmented Drive Field on a capital ship is a 0% bonus XP investment, I'm pretty sure, and I've currently got...14, 16, maybe 17 such ships in my fleet? That's a ton of bonus XP and SP I simply wouldn't have to option to invest in if s-mods didn't break the 2 logistics limit.
The logistics limit exists so that player actually make choices when configuring their logistics ships. Part of what makes Starsector compelling is the depth of the ship building side of the game. Spending story points to break that side of the game is shortchanging it in favor of what is essentially a worker placement mechanic that is done better on any of a thousand mobile games.
I barely made any choices prior to this patch, though. ADF/MS to get burn speed up to at least 9, expanded cargo/fuel for dedicated freighters/tankers to increase capacity (assuming MS was present, otherwise the maintenance cost increase put a stop to that), Efficiency overhaul if there was space left...and that was it. The closet I got to "choice" was putting ADF and EO on Colossi to have cheaper freighters at the cost of being visible from Domain space, which is of questionable value when out exploring where at least every other random fleet wants to kill you. My surveying ships used to be my Hammerheads just because putting the hullmods on actual logistics ships was never an option. Never enough room.
Now? With High Resolution Sensors changed and a skill which obsoletes half of MS introduced I've got a lot more options available, for logistics ships as well as combat ships since I no longer need to dress up combat ships as glorified surveying platforms. I've got actual
builds for logistics ships which depend on my skill selection. It's not a vast array, but it's an improvement nonetheless.