I am certain that there is lots of weird stuff under Tokyo, some of it built for military reasons, and some of it secret. However, is there some giant conspiracy responsible for building ten times as many tunnels as are publically known. Really I doubt it. And, there is this

Shun claims to have uncovered a secret code that links a complex network of tunnels unknown to the general public. "Every city with a historic subterranean transport system has secrets," he says. "In London, for example, some lines are near the surface and others very deep, for no obvious reason."

Well, the obvious first reason is that the ones close to the surface were built using cut and cover and the deeper ones using deep burrowing methods. And yes, there is an immense amount of underground crap in London, too. (For instance, there is an entirely different set of tunnels used by the post office for transporting mail, although this was largely a Victorian thing and isn't needed much any more). A lot of locations of tunnels can be explained by simple things, like the locations of sewers, however.

(via William Gibson)