There are several processes that can produce X-rays in a quasar, including thermal, synchrotron and inverse compton emission. Sometimes the X-rays come from the disk, other times from a jet. A disk (or something disk-like) is thought to be present in every quasar, while jets only appear in some of them.
It's true that an object falling into a black hole does not necessarily need to emit radiation -- there are orbits that pass through the event horizon. In that case, the gravitational potential energy would be converted to kinetic energy rather than radiation. However, disks are thought to appear in all quasars, so some of the gravitational potential energy invariably gets converted into radiation. There is a massive pool of energy and, whatever form it takes in the short-run (infall, magnetic fields, jets, winds), there is some radiation mechanism that can occur and make the process observable.