Excellent, thanks so much for the help, I'm happy to do this to help troubleshoot.
Modifying package.json to silence the warning was no problem.
I downloaded nwjs-v0.52.0-linux-x64.tar.gz and extracted the files listed, except the files nacl_helper_bootstrap and nacl_helper which were not present in the archive.
Launching the new HypnOS binary with these files = no more hitches!
However, the game now appears to be running windowed at its native resolution (480x270?), and fullscreening, maximizing, or resizing the window seems to make it render only a ~480x270 section of an upscaled view in the window's top left corner.
I have no real progress in the game to save, so if any further troubleshooting involves clearing my local config, that's no problem.