I suspect that a lot of that stuff goes into the void (ie disappears) for balance reasons. Otherwise what's to stop a player from killing merchants to get at stuff they shouldn't reasonably be able to afford yet? A clever player killing off a merchant to get at gear more powerful than what they should be able to get could wreck game balance, and denying you their money and good equipment for killing them discourages murderhoboing for the best equipment even if it is unrealistic
There are a lot of options to make sure you end up killing only the traders that are also possible ostile npc's (like the one chasing after Shaka, I don't remember her name, the thiefling, or the one in the Goblin camp) like position them in places where a kill would end up in a spread fight, or lower their attitude towards the player's character to the point they wont appear as merchants to the player).
This way is just illogic. At least they could put some ash in the inventory tab to show that the fight damaged the goods, but even if this could explain why items disappear the lacking gold still is just laughable (in one case the seller had more than 1000 gold tha puff just disappeared after the fight).