Yes, Microsoft can disable pirated games installed in your Windows 10 PC, but the real question is, will they ever do that? The company updated its End User Licence Agreement terms (a document that nobody ever reads) that it can disable any counterfeit software or hardware, and you agreed to them by upgrading to Windows 10.
The agreement now includes the following:
"We may automatically check your version of the software and download software updates or configuration changes, including those that prevent you from accessing the Services, playing counterfeit games, or using unauthorized hardware peripheral devices."
This agreement applies to Xbox One and Xbox Live too so it's safe to assume Microsoft will continue issuing Xbox software updates to block certain peripherals (hacked controllers, mod-chips etc) and pirated games. But it's unlikely the company would scan your PC to find a pirated copy of a particular game on your PC.