For me it's annoying when user posted questions on multiple sites without letting readers know about the posts. It would be great if I can mark such questions/users somehow. May be decreasing their reputation as well.
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We have this already in the form of moderator flags.
If you come across a question that has been cross-posted on another site, flag it for moderator attention and include a link to the cross-posted question. (You'll need to choose the "Other" option, which allows you to provide a free-form explanation.) They can close/delete the question on the site where it is least appropriate, and advise the asker not to post across multiple sites.
Repeated offenses or otherwise ignoring this advice would result in a permanent ban on their ability to ask questions. That seems like enough of a penalty to me.
As far as reducing their reputation, questions are automatically downvoted in many cases when they are closed. But don't forget about your own ability to downvote the question! And downvotes on questions are now free to help encourage people to use them where appropriate. A downvote reduces the reputation of the asker by 2 points.