Comment 7 for bug 587408

The upstream bug has been marked as WILL_NOT_FIX. The developer seems to not care about the use case claiming

"It isn't fair to say that eCryptfs won't work to encrypt user directories because very few people have 100,000 files in a single directory. This is the first time I've heard of this performance complaint."

The fact is any stat() call is slow so you just have to have a bunch of files being stat()'ed, they don't need to be in the same directory. As is obvious in the tests done by msznapka 10k files shows the slowdown nicely and that's not too hard to have in a home directory. My Photos/ has 40k files and a kernel tree has 37k files so this is hardly academic.

Switching to encfs may very well be a good solution.