did you ever consider the idea of using one big file
e.g. for vcs vault, instead of the very great number of
individual files you are currently using?
I'm just running a virus scan and it takes a considerable
long time to scan the IDEA vcs vault because of the huge
number of files there.
Also, I think, file access to huge numbers of individual
files will be slower than using one big file.
+ disk fragmentation will at some point be an issue,
regardless of how big your disk is.