Not just webgl, I think all hardware acceleration, even canvas2d, is disabled.
To answer your question, sort of. Node webkit does take parameters, but for some reason the --ignore-gpu-blacklist argument isn't working in the package file currently, Ashley's looking into why. If he can get that working then C2 will automatically use it when exporting to node webkit.
Until then, your only two options that I've been able to find are:
1: make a shortcut to NW.exe, edit the properties, add " --ignore-gpu-blacklist" (everything in the quotes, but not the quotes themselves) to the end of the target field, and run that instead of the exe. Downside - this doesn't help with previewing and the user could run the exe directly.
2: revert back to an earlier version of node webkit, I think it was somewhere around version 160 that it switched over to the version with vista blacklisted. That's what I've done.