Yes. All commands are stored into database (and loaded when user join the server).
Note that this disable standard ulx groups ( currently looking for a better solution for this ).
If you have a new command, you need to add into list:
open inc/commands.php
and simply add command in a new line. Than update groups to use the new (non-default) commands.
I will probably change concept in the new versions, so you can insert bans into database with standard "ulx ban" or "ulx banid" command (it will use both: flat file by default and database). Also, there will be synchronization between databases (auto) on each map change (or server start), so if you have old bans in banned_users.cfg it will be added into database.