During Operation Iraqi Freedom, many Iraqi command bunkers and suspected chemical-biological weapons bunkers were deeply buried underground and thought to be difficult to disable using conventional explosives. New HPM weapons were reportedly considered for possible use in attacks against these targets because the numerous communications and power lines leading into the underground bunkers offered pathways for conducting powerful surges of electromagnetic energy that could destroy the computer equipment inside. Because instantaneous HPM energy can reflect off the ground and possibly affect piloted aircraft above, much testing currently involves HPM devices on Unmanned Aerial Vehicles (UAVs), and on the Air Force Conventional Air ...
https://www.wired.com/images_blogs/d...iles/Ebomb.pdf
Unless, those underground facilities have no conduit from the surface they are not really safe havens. Even a radio antenna to the surface will serve as a conductor.