It's highly (99%) unlikely that it will affect any of your modifications. vBulletin's DB code is an abstraction layer in itself, so it covers the mapping of $db function calls to the underlying database adapter functions.
However, eventually I can see the standard mysql function being deprecated. Maybe not in vBulletin, but other applications who wish to use the more powerful database functions. I know Zend Framework requires PDO_MySQL or MySQLi to function.
It's a safe bet to use it.