I've found something related in debian/postrm, but I don't think it gets 
considered, when re-installing:
  case "$1" in
    remove)
       cd /etc/ssl/certs
       echo -n "Removing hash symlinks in /etc/ssl/certs ..."
       find . -type l -print | while read h
       do
         test -f $h || rm -f $h
       done
       echo done.
       ;;

You should take a look at /etc/ca-certificates.conf: it says that certs
should be installed into /usr/share/ca-certificates.

** Changed in: ca-certificates (Ubuntu)
       Status: Needs Info => Unconfirmed

-- 
ca-certificates removes all users certificates in /etc/ssl/certs
https://bugs.launchpad.net/bugs/114495
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