You would be surprised at how much water does leak through the subsurface of the earth, and air exhaled inside cenotes and caves does the same, only in reverse. How do you think massive underground aquifers get recharged? In some of the cenotes we've been in, there are pretty significant collections of air along the upper surfaces of the caves, but honestly, I've never worried about it. In some of the centoes there are open areas above the water level that you can actually surface into and take out your Scuba regulator, but I am not so sure that those pockets exist solely because of Scuba diving activity, more through the porosity of the earth above.
