I have two tests folders both wit many files and sub folders, one is on
a full disk encryption with TrueCrypt, another one is eCryptfs on a ZFS
RAID-5 array (much fast disk unecrypted).

I have a python script that stats files in a folder and its directories.

Under the eCryptfs, the script stats about 50k files, and it takes about 12 
minutes
Under the TrueCrypt volume, it stats about 800k files (yes, 16 times more), yet 
it takes only 1:15 minutes

So the TrueCrypt version is about 150 times faster? (at stating)

Therefore the argument that the slowness is normal due to statting a
large number of files is invalid.

A better explanation might be here:
https://bugs.launchpad.net/ubuntu/+source/ecryptfs-utils/+bug/654764
So it might be because of the design of eCryptfs.

Might give a try to EncFS and post the results

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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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