I believe there are actually some cool things they do with the extra space in the Objective-C runtime. It's been a while so I may be mistaken but I think they store the reference count in the pointer to avoid a lookup to a separate table. There might also be some trickery in storing NSNumber values in the pointer itself as well.
As the 64-bit CPUs used on the iPhone actually only have 33-bits of address space (undermining the benefits of having more address space ;P), Apple does use the extra space in a pointer to store "tagged" values in some cases, but for the most part this can be seen as a "mitigation": as the size of a pointer is now 64-bits, and as the alignment of a lot of things is now 64-bits because of that, processes are larger and heavier than on 32-bit systems, and thereby require more memory bandwidth. Sharing some of the bits of a pointer is essentially required to win back this lost performance. (Another great option is a 32-bit ABI using the 64-bit instruction set, as with x32 on Intel, but Apple did not go that direction.)
EDIT: Grammar