Secondly, the fan blades are made either from titanium or from carbon fibre. Atleast some of them should have survived in almost single piece, perhaps in very bad shape. The turbine core rotors are made from inconel or similar alloys, which can survive ALOT of heat and pressure, many of them should have survived.
As far as disintegration is concerned, yes parts will disintegrate but they don't completely disappear/vanish.
Thirdly, the turbo fan engine is not "mostly empty". First there is the outer most fan that provides most of the thrust. Then there's the compressor stages which contain more than just fans, they also contain stators and the shaft takes up alot of the space too. After all the compression stages come the combustors where the fuel is added and ignited. Then this hot gas goes into the core high pressure turbine and then more turbine stages which power the engine.
How ever there is not much behind the main fan, just a flow through casing.
In any case, big/bigger parts of the plane should have survived in the pentagon crash...