Most fans had deduced that the ghost buildings were a homage to the actual Twin Towers. This was strengthened by the fact when Spider-Man climbed the building on which the Twin Towers were reflected, players could see the game's version of the Freedom Tower.
The explanation, when it came, was boringly simple.
The game's cube mapping technique generates reflections. This method stores 'still images' from the game world, in a library. And, the reflections are an approximation of the images taken from this library.
The Twin Towers were just the reflection of the very building that Spider-Man was climbing and another building to the right.