| GOTY includes all the patches up to the time it was released, and I don't know of any really important patches that have been released since then. So you don't have to DL any patches unless you really feel compelled to stay up to date.
There are many caves & forts that are not linked to any quest, and in most cases it doesn't hurt to loot a place even if it will be used in a quest later. There are a couple notorious exceptions, though. Don't raid Swampy Cave or Sandstone Cavern until you get the quests that send you there, or it might break the quest.
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Can the answer to this question be "No"? | 
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