How do we discourage all these simple questions that are duplicates of other questions? A lot of the more experienced people know that simple questions are great for getting lots of reputation from, so way more incentive to answer it rather than close it.
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If a question is, in fact, a duplicate, then closing it is the right thing to do. There's no point in building up a bunch of answers in multiple locations to the same question.
You express concern that there exists an incentive for people to answer these duplicate questions in the hopes of earning easy reputation, rather than voting to close them as a duplicate. I agree that this "problem" does exist, but I think it solves itself. Recall that the closing of a question is generally the first step toward its deletion, and that when a question is deleted, it takes all of its answers with it. That means that the answers those users posted in the hopes of gaining some easy rep will be [eventually] removed, taking all of that reputation gained with them. Even better yet, we're now making these reputation fluctuations happen immediately, rather than having to wait for a manual recalculation, which might have been quite rare indeed under the old system.
I don't really see a lot of duplicate questions that miss getting closed. I'm sure there are a few in some of the less popular tags, but there are enough high-rep users with close vote privileges on SO to make this not a real problem. Furthermore, once a close vote has been cast, those questions begin to appear on a list accessible to all 10k+ users. A significant percentage of us go through that list regularly, casting our own close votes where appropriate and hastening questions toward their impending closure.
If you do come across a stale question that should be closed, hasn't, and is unlikely to amass the 4 other close votes necessary, you should consider flagging it for moderator attention, explaining your rationale. If those of us who are conscientious and care do our part to keep the site clean, history tells us that generally things will work out in our favor, even if there are some users who try take advantage of the system.
By doing what we do now: down-voting to oblivion, closing, and--if necessary--letting the question ban algorithm do its job.