I would imagine you add something to /etc/e-smith/events/actions/nethserver-duc-index for exclusions.
That’s the file that’s run with the daily cron job to recalculate disk usage and I believe it’s just rerun manually when you click the update button in the web gui.
edit: found it! change this line:
/usr/bin/duc index $INDEX_DIR --database=$DUC_DB
/usr/bin/duc index $INDEX_DIR --exclude=opt --database=$DUC_DB
Reference this for more cool stuff you can do!
Edited to correct lines to edit. Thanks @Nas!