Not sure if this will help for ntfs, but I changed my mlocate cronjob to
launch updatedb.mlocate with an "idle" io priority. So the last lines of
/etc/cron.daily.mlocate look like:

##

# See ionice(1)
if [ -x /usr/bin/ionice ] &&
    /usr/bin/ionice -c3 true 2>/dev/null; then
    IONICE="/usr/bin/ionice -c3"
fi

$IONICE /usr/bin/updatedb.mlocate


This should probably be accompanied by a nice 19, to also reduce actual 
userspace CPU stress.

-- 
updatedb.mlocate causes long time high ntfs-3g IO usage
https://bugs.launchpad.net/bugs/362809
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