The largest problem with the article you linked to is the kind of bunker busters it refers to are pretty standard. It's a bomb that hits the surface and explodes. My assumption was you were talking about something a bit more complex that propels the nuke down into the stone THEN detonates. But it also outlines that they were created to penetrate purely concrete facilities. Not penetrate a mountain of stone. And elevator shafts are protected by millions of tons of stone overhead. Like, nothing from that article is going to impact government/military brass level bunkers. Not without an earthquake. Though it may collapse it, if they're lucky, so they can't get out. That's it.
I understand what you're saying. Pearl Harbor was a hell of a lesson not to be too confident in your safety measures, but honestly, too many government systems have been hacked at this point for me to believe that opposition efforts are designed to hit bunkers that aren't particularly relevant in the first place.
I was talking about a penetrator. Then I linked the article because it shows both bombs and bunkers getting bigger / stronger which is all part of the arms race.