It is common to see abnormally shaped class D which has been designed with the Instrument procedures that go along with an airport in mind. Sometimes you will see a box outside the normal cylinder, extended out from the centerline of a major runway. This is to keep the aircraft in a smooth transition between class E to D, without scraping the top of the G airspace which comes up to 700 ft AGL at those areas... (inside the magenta "fade", outside the blue dotted line).. That way ATC always has "control" over the aircraft.
So no, Class D isn't always a cylinder.. But no, I haven't seen shelves. Sometimes you'll also see those same boxes, except defined in magenta dotted lines... Inside this space. This space is not class D, its class E, but instead of flooring out at 700 AGL, it goes all the away to the ground... The purpose of this, again to assist in the aircraft on approach to transition from class E to D, without wandering into G.
Hope this helps!!