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.

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https://bugs.launchpad.net/bugs/587408

Title:
  Ecryptfs is very slow at listing directories with many files

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