The capability you want simply doesn't exist in headless NetLogo 3D.
I don't think we ever even explored how difficult it might be to add. It appears to me from googling “headless JOGL” just now that it would be possible. I think it's extremely unlikely it will happen though, unless it comes in as an open-source contribution, or unless someone offers funding for it.
Perhaps you could solve it by running the NetLogo 3D GUI on a virtual X server. (Note that I don't actually know if Xfvb and JOGL play well together, but it seems plausible that they might.)
Or, you might consider generating your 3D visualizations using this instead: https://github.com/fstonedahl/RayTracing-Extension , in conjunction with POV-Ray.