I think that would be default for new DB's - which means there could be some MyISAM tables that have managed to 'sneak' into the DB for Moodle depending upon how long you've been running Moodle.
It doesn't hurt to run it.
php admin/cli/mysql_engine.php
is the same as running it with the -h (--help) switch. Given the script no parameters.
php admin/cli/mysql_engine.php -a
shows a list of available engines.
php admin/cli/mysql_engine.php -l
shows a list of moodle tables and that tables engine.
If they are all InnoDB then no worries.
If they aren't, then run:
php admin/cli/mysql_engine.php --engine=InnoDB
They recommend running as the apache user and show that in the examples, but it will run as root user without issue.
'spirit of sharing', Ken