As I've been raiding and looting various scattered caves around Skyrim if the said cave was emptied of enemies and loot that if a quest later on in the game required me to go back there would the cave itself reset and the quest still be activated? Or would said quest be nullified?

Be very wary. I have items stuck in inventory and quests not being able to be finished from doing dungeon crawling in my character's infancy stage(s). Only to find out crawling busted something HOURS later into the game.

Oh man that is bad news, I'm sorry to hear you've experienced this. Many thanks for the heads up though. Hopefully the next patch will address this!