I am setting up a new modlist, and testing as I go along. Last mod I installed was The Great City of Winterhold (which is great BTW) but when running around it, I noticed a few naked NPCs.
Then I coc to Whiterun, to do more testing and Aela, Farkas and Ria were fighting the Giant on the farm with nothing on, and no weapons (they were fighting unarmed!)
I opened Aela on SSEDIT and she has no issues - otft record, inventory with weapons all seem in order. Wondering what is causing this and how I can fix it.
Is it a bad sign if the Base and the Ref are referring to different ESPs?
Edit 2: I worked it out. I had the first version of this mod - https://www.nexusmods.com/skyrimspecialedition/mods/109152. It was applying to NPCs, and they were naked because they were too low level for their gear. Because it is all script injected, it wasn't clear that there were any issues when looking at SSEEdit. The dangers of runtime-patching, manifest!
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.
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
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.
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