When the shuttle, a plane, or any other object travels through air faster than the speed of sound, it creates shock waves that produce sonic booms.
Such shock waves are produced at the site of any discontinuity in the craft, such as a wing, but the loudest ones are produced at the nose and the tail.
All planes produce two sonic booms, but a jet fighter, for example, is so short and so close to the ground that the two are superimposed and we hear only one.
The shuttle is more than 100 feet long, producing a small time separation between the two booms.
Furthermore, the two shock waves diverge slightly. When the shuttle is very high, this increases the separation between the booms.