If someone else comments that a question is a duplicate, if I agree that it is a duplicate, should I also flag it as duplicate? I assume it has already been flagged at least once in this case. However, I would think having multiple flags on it would help the moderators see that it probably really is a duplicate vs. a similar question. If a question only has one duplicate flag, it might take a little more looking into.
First of all, flags for closure are typically handled by regular users, not just moderators.
Recommended closure flags (including duplicate flags) push questions into the Close Votes Review Queue, which can be accessed by users who have privilege to cast close and reopen votes. Once you obtain this privilege, you will no longer be able to flag for closure, and will instead gain the ability to cast close votes.
Multiple flags will raise the question's priority in close vote queue, so there is nothing wrong with flagging multiple times.