Let me try rephrasing what I'm trying to say.
The CPU's bitness has does not do anything in terms of making things faster. 64-bit CPU doesn't mean your apps is twice as fast. It just means it can read more than 4GB of memory and mapped data files, nothing more. Since iPhones doesn't use that much memory nor deal with those file sizes, it's pointless.
However, Apple's 64-bit A7 CPUs are much faster than the previous CPU is because of the brand new SoC that's based on ARMv8 which comes with the massive increase of hardware registers. ARM v8, which is a brand new ISA to kickstart the 64-bit ARM series of Chips.
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Also this means that fat binaries will become more fat, armv7, armv7s and armv8 binaries in one app. It also will make iphone5s firmware a huge one, since it needs binaries of all 3 arches to be able to run old apps.
We don't know anything about fat binaries yet. Developers will have to upload fat binaries but the App Store can selectively download a specific file to the iOS devices, 64-bit only app to 64-bit iPhones and 32-bit only to 32-bit devices.
At least, I hope Apple does that since iPhones often have limited resources for them.