Innodb is indeed faster when it comes to complex queries that use a lot of joins, but on the other side innodb uses a lot more ram. As ISPconfig dont use complex queries and does not require any of the innodb features, so it does not benefit from innodb and we decided to keep the RAM for the applications instead of wasting it for the controlpanel.
I also thought that scripts were agnostic as far as the table engine being used? I've not come across any script which cared whether it was myISAM or InnoDB before, only an old one which used MyISAM indexes.
Thats almost always the case, but in some scenarios the engins seem to differ when it comes to inserting data into the table. I experienced that a operation might succeeed with myisam while it failed with innodb, maybe myisam is a bit more fault tolerant.