changing circulation status from OVERDUE to MISSING automatically

Is there a way to set up the system so that when an item is say, 12 weeks overdue, its circulation status will change to missing?

Sorry, there's no such setting for that. You'll want to periodically review your TinyCat Admin > Transactions > Statuses page to view all of your "Overdue" items, and decide from there what you'd like to mark as missing. I hope this helps!