Capitalizing the directory names is a way to guarantee that they will not conflict with the directories in the legacy file system hierarchy.
I find that to be quite a weak argument. Avoid conflicting with known standard structures such as "bin" ans "etc" if necessary (which it isn't—you could theoretically run all applications in a filesystem namespace mimicking their expected structure), but that should be the only concern. Non-standard structures might clash anyway (capitalized folders in root does unfortunately occur).
The known standard does change though. For example, since Gobolinux came out in 2003 the FSH added /run and /sys...
Case insensitive auto completion FTW.
That's a nice convenience feature, but when it starts to become a necessity, you should really reconsider your naming schemes...