No duplicate folders as far as I know, I do the standard "delete the old folder and replace it with the new one" every time, and I don't really use Dev Mode. I kept getting the same crashes no matter how many times I downloaded from the link so if no one else is getting the same thing it must be on my end.
gotten it to work now, but I had to jump through a few hoops.
Basically I had to add the info and files for the following ships/hulls from the older 1.03.39b version to the newer 1.03.40b that didn't have them:
Their graphics were there, but they were missing from the hull and variant folders as well as the descriptions (strings) and ship_data files. After I copy/pasted everything over it started working.
No idea why the game insisted they need to exist even if they seem to have been removed (I was starting a new game after all).
Spoiler
"starpocalypse",
"$$$_lightshow",
"AMPP",
"pantera_ANewLevel40R",
"Adjusted Sector",
"alkemia-armoury",
"A_S-F",
"Angry Periphery",
"anotherportraitpack",
"ARSWP",
"apex_design",
"ash",
"Arkships",
"armaa",
"raccoonarms",
"AzurlanePortraitPackSSR+NoJail",
"battle_music",
"BSC - Drone Refits",
"timid_admins",
"better_deserving_smods",
"better_variants",
"BSC",
"blackrock_driveyards",
"Blockade",
"bluefriendballs",
"bruh_moment_console_commands",
"ORK",
"CVFEHE",
"CVFEH",
"CaptainsLog",
"CFT",
"clearCommands",
"chatter",
"cmutils",
"timid_commissioned_hull_mods",
"su_Concord",
"lw_console",
"timid_cum",
"istl_dassaultmikoyan",
"hm_flagpack",
"diableavionics",
"Diktat Enhancement",
"domhist",
"dronelib",
"seven_nexus",
"Everybody loves KoC",
"exoticatechnologies",
"a111164_ExtendPack",
"su_FairSMod",
"fast_engine_rendering",
"HHE",
"ruddygreat_HullmodFilters",
"fleetsizebydp",
"sun_flux_reticle",
"forge_production",
"fqol",
"gflportraitpack",
"GrandColonies",
"Guardian_prototype",
"HMI",
"HexShields",
"hte",
"hiigaran_descendants",
"sun_hyperdrive",
"illustrated_entities",
"immersionFriendlyPortraitPack",
"IndEvo",
"interestingportraitspack",
"Imperium",
"timid_xiv",
"JYD",
"kadur_remnant",
"kazeron",
"LTA",
"lw_lazylib",
"leadingPip",
"ArkLeg",
"lights_out",
"lobster_proliferation",
"lockedAndLoaded",
"luddenhance",
"lunalib",
"MODCalveraSystem",
"exshippack",
"exshippack_armaacompat",
"mag_protect",
"MagicLib",
"miner2049er",
"Mayasuran Navy",
"MissileShipOverhaul",
"missingships",
"dp_mnemonic_sensors",
"molecularreplicator",
"more_hullmods",
"more_ship_names",
"ness_saw",
"nexerelin",
"yrex",
"objects_analysis",
"luddandlions",
"officerExtension",
"JYDR",
"ORA",
"pn",
"pearson_exotronics",
"periphery",
"wisp_perseanchronicles",
"planet_search",
"portrait",
"pt_qolpack",
"roider",
"swpXIVLG",
"tahlan_scalartech",
"Scrapyard",
"SCY",
"Seafood",
"secretsofthefrontieralt",
"SEEKER",
"holdsforall",
"swp",
"shush",
"mayu_specialupgrades",
"speedUp",
"StarfarersWorkshop",
"SPAIP",
"sun_starship_legends",
"stelnet",
"StopGapMeasures3",
"sss",
"Sunrider",
"superweapons",
"supportships",
"tahlan",
"Terraforming & Station Construction",
"star_federation",
"TBJ",
"timid_tmi",
"TORCHSHIPS",
"transfer_all_items",
"vesships",
"underworld",
"uaf",
"US",
"UnofficialDiableAvionicsPortraitPack",
"vic",
"variants_lib",
"vayrashippack",
"weftinships",
"whichmod",
"audio_plus",
"mir_ed",
"astroidships",
"ezsadditionalcharacternames",
"shaderLib"