Pipes in mid-air and pipes leading into/out of Bowser's body are seriously confusing.
I don't recall the website, but there used to be one that discussed theories for nearly all things in the Mario world. They wrote it like a report (actually, they wrote as if Professor Gadd had been writing it), and one theory they had for the pipes were these mysterious stones that they called warp stones. The discovery of the warp stones lead to two mushroom people testing the stones by placing one in a cup full of water and another in an empty cup, and watching as the water vanished from the first cup and appeared in the second.
Anyway, I've always liked the warp stone theory, so maybe that's it..