I think closed, non-PTIJ questions should be left out entirely. They're closed because they're a bad fit for the site, so adding them to the siyum post is just unnecessary noise.
PTIJ questions should definitely not count towards the goal of having a question per perek. They can be added at the bottom of the masechet's post, in a labeled spoiler section.
If a question that is closed as a duplicate contains some extra information related to a mishnah, but the main question doesn't (as pointed out by DoubleAA), my proposal is as follows:
- If the information improves the question, it should be edited into the main question.
- If it's extraneous, then it probably would have been edited out of the duplicate if it hadn't been closed as a duplicate, so it shouldn't count.
- There could be some corner cases not covered by either of those two possibilites, where it actually makes sense to refer to a duplicate (e.g. why don't Jews consider Bar Kochva Mashiach, answer refers to נלכדה בתר, then it was marked as a duplicate of the main reference question), but they should be very rare and I would take those on a case by case basis.