Hi, thanks for your question. There's three parts to it really:

• Realistic expectations. It is already very difficult to get early (iPhone OS 2) games working, and each new iOS version we support will only increase the difficulty; the OS and apps for it only get more complex with time. 64-bit support first appears in iOS 7, but it would be a miracle if touchHLE could support even iOS 6.
• Implementation simplicity. touchHLE's code assumes 32-bit throughout. Making it support both 32-bit and 64-bit would make many things more complicated.
• Lack of interest in that era of apps. The touchHLE project exists to preserve an older, less cynical era of mobile gaming. By the time you have 64-bit-only iOS games coming out, the mobile app space had fully decayed into its current freemium economy where good games are rare. Moreover, later titles are usually available on Android too, and there's plenty of good emulation solutions for Android titles.

I hope that gives you some insight!