ISPConfig 3 has two different configuration files, one for the server part and one for the interface.
Interface:
/usr/local/ispconfig/interface/lib/config.inc.php
Server:
/usr/local/ispconfig/server/lib/config.inc.php
The mysql root password which is only used to create new mysql databases is stored in the file:
/usr/local/ispconfig/server/lib/mysql_clientdb.conf