For the first question, feel free to use packetcollector when playing on live and fix all those 'problems' with items.
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I haven't done a ton of research into how the loot tables work
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You gave yourself an answer to your second question.
a mob drops some stuff only if some stuff has been added to it.
- when its spawned from scratch by a GM
- or in the DB.
Instant repops : see npc_types table, there's a field that specifies the respawn time. Check also if there's not 2 or more npcs spawned instead of only one. There's a post in the world building forum about that.