What is the purpose or historical significance of /usr/64, if any, on OS X?
/usr/64 never existed in OS X, go ahead and remove it.

There was, however, a directory called "lib64" (or /usr/local/lib64), which offset /usr/lib. This was found on some Linux operating systems back some years ago, when the transition from 32bit to 64bit was still in its infancy. It may still be used today as a remnant of that era. Microsoft Windows also had a similar structure, separating 32bit from 64bit.

OS X has never used such a separation of libraries or even executables.