A tunnel filled with hydrogen has a large surface area for potential leaks.
Suffice it to say, the challenges of an electrically grounded hydrogen tunnel lined with heavyweight materials using modern technologies & sensors are a hell of a lot different than the challenges of an ultra-lightweight, ultra-thin flammable gas bag before the advent of plastics, in an electrical storm.
A tunnel filled with vacuum has it a hundred times worse, because you're dealing with 15PSI trying to get in rather than 0PSI pressure difference diffusing out. We already regularly use larger-molecule methane at thousands of PSI.
Obviously a modern hydrogen tunnel would be much different than a zeppelin, and have different challenges. Still, 400 miles of 10-foot diameter tunnel would have plenty of opportunities for problems (whether it's evacuated or filled with hydrogen or something else). I'm not sure an evacuated tunnel is necessarily worse from a safety standpoint, though. It might be harder to engineer, but the failure mode seems safer. A hydrogen tunnel means that a leak will mix hydrogen with an oxidizer. If it's at 0 PSI, this could mean a leak lets oxygen into the tunnel (either due to high-pressure weather or due to hydrogen rising from the leak, leaving a low-pressure environment in the tunnel). If you wanted to fill a tunnel with hydrogen, I think it would be wise to keep at least a small positive pressure to ensure than any leaks are outward only.
I'm totally unclear why methane stored at thousands of PSI is relevant. Is there some 400-mile long, 10-foot diameter, above-ground methane tunnel I'm not aware of?