You're not given the option to skip unique hostile encounters. Unless you're referring to the oddball +1 generic weapon found on random encounters; far better would be found in normal areas. I skipped probably 9/10 encounters or more and don't feel I missed anything. Baldur's Gate had such random encounters as well. And Fallout. Lot of quibbling over nothing.
Sorry who is talking about random encounters? I am talking actual fixed maps that are duplicated. If you couldn't see the duplicated maps then you were simply not paying attention. The best example of this is the overland map with a cave in the top right corner. That map is duplicated about 5-6 times (if not more). There are a ton of other locations that are duplicated. Every village/town/city are duplicates that even share the same vendor and interior maps. The only thing unique about them are the artisans.
And these maps often have very good loot inside, so aren't really skip-able for the reasons I gave before.
Not as bad as Dragon Age 2 though BG2 had a couple but nowhere near as many as Kingmaker.