Bits can be easier to change than atoms. Bits do not. Furthermore, sometimes atoms are in a place but can't be seen when we would like to see them, such as wires or pipes in walls. Placing the information in those places with bits can provide new ways to view and interact with hidden atoms. Furthermore, associating information with places has certain advantages over simply putting the bits in a standard computer file system indexed by name, hierarchy, or content.
Real space can be a powerful mnemonic device for remembering where things are.
Placing information in real space can make interacting with certain information more natural than on a 2.5D desktop metaphor.