Should the pins marked GND in the "HMC Pin Assignment for DDR3/DDR2" section of the Pin-Outs file provided by the Hard Memory Controller (HMC) be connected to GND?

Yes, pins marked GND in the HMC Pin Assignment for DDR3/DDR2 should be connected to GND. 
The process for the corresponding pins is the same as the "Unused Pin" setting. 
" Please refer to the following contents of Macnica Online Service for the "Unused Pin" setting.

• Unsed Pins Overall Settings
  • (Reference) Quartus Prime Beginner's Guide How to set device options
    • (2-4. Unused Pins page)
• Unused Pins individual settings
  • (Reference) Quartus Prime Beginner's Guide - Pin Assignment Method ver.15.1
    • (4) How to set the attributes of unused user I/O pins

Check the pin numbers in the "Resource Section" > "All Package Pins" in the Compilation Report.

Since the default setting is "As input tri-state with weak pull-up" 
Compilation Report also shows "RESERVED_INPUT_WITH_WEAK_PULLUP". 
In this case, connect to GND.

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Category: External Memory Interface 
Tools: Quartus® Prime 
Device: -