As I understand it, this is intentional!  I agree that in theory this
aught to work, but mlocate would need to be completely redesigned to
address the security issue.  Note that 'ecryptfs' is in the 'PRUNEFS='
line of the default /etc/updatedb.conf file.  I suppose you could edit
this file to 'fix' this problem, but know that your encrypted metadata
(file and directory names) will be readable by anyone who steals your
computer.  See:

  https://bugs.launchpad.net/ubuntu/+source/mlocate/+bug/372631

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mlocate does not work as expected on encrypted disks
https://bugs.launchpad.net/bugs/578303
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