Check their inventory with informative console. If they have their stuff but don't equip it, check your skeleton/npc/race overhaul mods
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So they DO have items in their inventory, just not equipping it. Not just armour, weapons also. I thought it could be AI overhaul, so I ran the synthesis Patcher as a test, and that didn't fix it.
https://i.imgur.com/BRarjGU.jpeg
This is annoying AF
Your problem is relatively familiar. It seems we have an inconsisteny in what is given to NPCs equip, and what can be equipped. Sometimes this comes from the new item given to them is missing their target model completely. It's different from a simple missing texture.
The mod that's creating this issue is also the one that touches each of your errored (nude) NPCs. Since it's on major vanilla characters, we know where we can start looking, specifically at the items placed in the problematic NPCs' inventory, like the other user said.
Based on what you said, that you've installed a mod list, I think the most likely problem is that your new clothes and weapons plugin(s) are being over-written by something different later in your load order.
If you do the old binary two-step and disable half your new mods, or armor mods, and try to replicate the issue, that usually helps. You'll notice that everyone will be back to normal once you have deactivated the culpable plugin from your mod manager. After this we simply and patiently enable half of the newly disabled plugins until we see naked NPCs again (yay). Finally you've singled out the broken plugin, you can either reconfigure it's load order arguments or FOMOD or just eliminate it completely.
Good luck and godspeed
Yeah I guess I do need to do that. Thing is, I haven't added any new Armor or Clothing mods yet, I leave those to the end of the process when making a list.
Binary search it is. Jeeze. I have been adding mods like crazy since the Christmas break, I am assuming it started sometime around then. Oh well.
Start a new game and check if the equipment is right. If it is, you most likely changed object IDs by swapping mods or replaced a still running AI script
all of this is on new games. I haven't finalised my LO yet, haven't started my run. I am coc'ing into whiterun from the title screen here.
Then it could be a incompatibility with a skeleton replacer / equipment mods / AI mods... If your loadorder isn't finalized and there is no save to break,just disable mods in ~50 batches and narrow the faulty mod down
Ha, I have like 1200 ish mods. Think I am gonna need to start with larger batches.
You could probably do halves
I've encountered a similar thing before. Your situation might be different, but the culprit on my end was actually SPID, or, more specifically, multiple SPID inis distributing outfits to the same NPCs.
Skyrim can't have more than one outfit for an NPC, so if something, for example SPID, distributes two to the NPC, things get funky and the NPC refuses to equip anything. Have a look through your SPID inis for ones that are distributing outfit records, see if that's causing it
holy crap am I reading correctly that you are running 1193 mods?