Haven't played for a long while, nice to see a new update but I'm definitely not liking that 2 dock hullmod only limit, my polymath/jack-of-all-trades playstyle does not agree with it not one bit. Hopefully I can still brute force them onto my main superships like before but still it'll take a while for me to get up to speed with this game's modding again so I guess I'll stick to previous version for the time being and save my nerves for now.
Loadout Design seems like a good place to add the ability to equip more logistics hullmods (as Megas suggested before), though it's already a bit of an overloaded skill.
Oof! Ouch.. just looked at ship_design.skill (looked in ShipDesign.java too) and I'm not seeing an obvious way to increase the limit. I'm no coder, I can only copy and paste and more-or-less understand existing/done stuff but not make up new stuff from scratch. Adding those dock hullmods as built-in stuff on my custom ships is easier for me so I'll go with that instead as a start.
Agh, looks like weapons and ships have more tags too so porting my ship or two over is also easier said than done now. Bleh, onto to my plan C or D then; Making a new supership out of one of the REDACTEDs and call it even.
Alrighty, another edit and some lite modding later and I gotta say it ain't that bad because the new REDACTED capital ship is an awesome tool of destruction, especially the converted playable version of it I just made. Time to go full Dalek and exterminate with it.