So this shopkeeper had all this stuff I couldn't afford and I tried to pickpocket him but none of the stuff was on his person and I can't find it anywhere in his shop. Where do they keep their stuff? I killed him but still can't find all the stuff he had for sale.

I'm not sure the full inventory is in the game world.

You can't steal from a shop inventory.

Put a bucket on his head and it will all become clear ...

unimersive
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Ah, Morrowind, I will forever miss you.

Does that basket trick actually work? I need to try that.

I believe you actually can, just not everything. I've noticed as I buy stuff, things that are lying around the shop disappear. Haven't tried stealing something lying around and then checking the shop inventory though.

I just tested it. You can steal from a shop's inventory so long as the item is being shown out there, otherwise you can't (I saw a shopkeeper had a draught of health among what he sold, stole the one he had on display and checked back, he no longer had it).

They most likely did the same thing they did in OB, the shop's inventory is kept in a chest underneath the store that is only accessible using noclip.

See in this shop there was stuff in the shop that wasn't in his inventory and all the expensive items (like 3000 gold enchanted items) are nowhere to be found. I really want those items but they're just not there...You're telling me I have to go honestly earn like 15,000 gold and buy them? From what, his corpse? Because I drove a mace through his head and for what, an empty store.... Laaaaaame..