Is there an industry standard serial hardware identification protocol?
Is there any industry-standard, or at least widely accepted, method for sending an ID request and receiving an ID response? 


Not available for COM ports - and I personally had software installed at one point that tried to do this (old mobile fon stuff), which was VERY annoying.

But most devices are actually connected via USB. USB has both VID:PID to identify the device type (and select a driver) and an (optional) serial number. That sould be enough to id those µC, right? Sadly, it is rather difficult to go from USB id to COM port and vice versa in software.

My recommendation for new designs: Ditch the COM port and use USB directly with an USB-enabled µC and WinUSB as the driver. No need for custom drivers or inf files, see Microsoft OS Descriptors.