> please explain why its a security problem?
Because a database with all the filenames is stored under /var/cache/locate/
So some stranger could guess what files you have in your encrypted /home 
partition, if /var is not encrypted.
I resolved this for me long ago by replacing /var/cache/locate/ by a symlink to 
some place inside /home where the database is stored now. But now me affects 
the missing indexing of encrypted drives aswell.

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https://bugs.launchpad.net/bugs/1205690

Title:
  Default settings for updatedb.conf do NOT index encrypted home!

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