Out of curiosity, I cooked up a version of git which used a flat base32, instead of base64, repository. The goal of this is, of course, to provide for compatibility with case-deficient filesystems.
The answer is that the base32 format is measurably slower than base64, with a cache-hot checkout time of 19.19 seconds (as compared to 15.68 for base64.) So the length of the filenames does matter.
Anyway, I have uploaded the base32 patch onto kernel.org, and I have moved all the git patches into:
ftp://ftp.kernel.org/pub/linux/kernel/people/hpa/git/
At this point, though, I would recommend the base64-flat patch.
-hpa