Hyper key functionality can now be achieved in Sierra with Karabiner-Elements alone, so there's no need to bring in Hammerspoon: Now Possible: macOS Sierra (10.12) Hyper Key with Karabiner Elements
Since that post Karabiner-Elements has even been updated to include proper GUI support for such complex modifications:
Once you've set up the hyper key in Elements, you don't need to set a USB Device Key trigger in KM to use it. Just set a regular hot key trigger using your new hyper key like you would any other shortcut:
