I have read very similar questions, but not exactly this: a new question is a duplicate of an older question. However, when I try to flag, I get the message This question does not have an upvoted or accepted answer.
Since the flag button is disabled, I guess that the correct behaviour is to let the new question live, to see if it is luckier, right?
(I know that, in this case, the two questions are not identical to the letter, but imagine they were.)
Yes, the idea is that usually the new question can stay open in the hope of attracting an answer. It can still make sense to point out the other question via a comment.
This assumes that it appears the new question was asked in good-faith. A user repeatedly asking the same questions is frowned upon. (In this regard, note that the restriction you quote does not apply when the same user asked both questions.)
If in some special circumstances you think the question should still be marked as duplicate, you can flag for moderator attention explaining the situation. (A moderator can override the restriction you quoted above.) Such circumstances would be an accumulation of (near-)identical questions, be it by happenstance or by attempts to circumvent the rule mentioned in the second paragraph.
