New satellite and aerial surveillance technology has made it more difficult to hide construction of these underground facilities, and especially difficult to hide the entrances. This makes it possible to use a "functional defeat" strategy. This approach uses smart bombs to knock out the entrances and outside sources of power, water and the like. If the underground facility is so deep that it can't be reached by a non-nuclear bomb, it's not so deep that it cannot be sealed off from the outside world. An additional option are EMP (electromagnetic pulse) weapons. These bombs get their electromagnetic pulses into the bunker via air and power ducts, and disable electronic equipment. These ducts can also be hit with smart bombs, to make the bunkers even less useful, not to mention uncomfortable.
The major weakness of "functional defeat" is its dependence on good intelligence. If the enemy bunker was built while surrounded by sufficient secrecy, "functional defeat" will be defeated. The North Koreans, for example, have been known to built several underground complexes close enough to each other to share entrances. The North Koreans are also reported to have built emergency exits to many complexes. These are tunnels built to within a few feet of the surface (or mountainside), and then equipped with explosives so a breach to the outside can be created quickly.
Even penetrating bombs with nuclear warheads have their limitations. Such bombs only go a hundred feet or so into the ground before the nuke goes off. There are known deep bunkers that are safe from everything except a very large nuclear explosion. But a nuke that size would be throwing lots of radioactive crud into the atmosphere, which would spread the radioactivity all over the planet. This is counterproductive if you are trying to limit the proliferation of nuclear weapons.
Thus the use of good intelligence (which is expensive and hard to get) and smart bombs to achieve "functional defeat" is increasingly seen as a better option than nuclear warheads.
American Department of Defense efforts to get Congress to allow the building, and use, of nuclear "bunker buster," bombs has been difficult. Such weapons are seen as necessary to prevent use of nuclear, chemical and biological weapons by militant and unstable nations like North Korea, Iran, Iraq and Libya. In the past year, two of those nations (Iraq and Libya) have given up their threatening ways. But that still leaves Iran and North Korea, both of which are known to have received nuclear weapons manufacturing assistance from Pakistan. Both nations are also known to have chemical weapons. North Korea and, to a lesser extent, Iran, have built weapons research, manufacturing and storage facilities deep underground. This protects them from bombing and observation. However, as both the North Koreans, Iranians (and Libyans) have discovered, you can dig, but you can't hide.