New way

can very easily be done through DirectAdmin with DA 1.47.0 and newer.
http://www.directadmin.com/features.php?id=1696

---

Old way

If you need to empty your Message System list due to oversize, you can do so by running the following for an Admin:

cd /usr/local/directadmin/data/admin
echo -n "" > tickets.list

or the following for a User:

cd /usr/local/directadmin/data/users/username
echo -n "" > tickets.list

---

For either tickets.list file, if you don't wish to remove all tickets, and keep the newer ones, you could use something like this, for example, to keep the 500 most recent tickets/messages:

cp tickets.list tickets.list.backup
tail -n 500 tickets.list.backup > tickets.list
rm tickets.list.backup

which would simply dump the end of the file, which contains the 500 newest entries.