Looks like a performance bug has crept in recently. Auto-Stack on 1185 photos is instantaneous in my LR 8.2.1 but takes over two minutes in my LR 9.3.
I filed a bug report:
Please add your constructive opinion to the bug report, and be sure to click Me Too and Follow in the upper-right corner. That will make it a little more likely that Adobe will prioritize a fix, and you'll be notified when the bug's status changes. (Safari users, uncheck the option Safari > Preferences > Privacy > Prevent Cross-Site Tracking or use Chrome or Firefox.)
As an inconvenient workaround, try waiting for several minutes to see if Auto-Stack finall becomes responsive.
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