Being able to flag is not dependent on a person's reputation, so flagging is especially helpful for users who do not have the appropriate reputation to vote to close.
If you can vote to close, you ought to do that instead of flagging unless the question is so egregious it absolutely needs to be dealt with outside the normal community moderation channels. In those cases, you should use flag for moderator attention, not the pre-canned close flags, to explain what is so bad about the question.
And, as Popular Demand pointed out in the comments, attempting to flag for the same reason as a close vote (rather than using the free-form flag for moderator attention or the other flags like spam) will be converted into a close vote anyway.
So, a general guideline:
- Do you have enough reputation to vote to close?
- Yes: Go to step 2
- No: flag it for moderator attention.
- Does the question (or its activity) actively harm the internet by virtue of it being left open (or even existing)?
- Yes: flag it for moderator attention.
- No: vote to close.
But being a duplicate doesn't necessarily make the question harmful: in fact, some amount of duplication is even encouraged. Check out Jeff Atwood's post, Dr. Strangedupe: Or, How I Learned to Stop Worrying And Love Duplication for more information about the benefits and nuances of duplication.