To prevent any consistency issues please ensure that InnoDB is configured as default MySQL engine (instead of MyISAM by default) before launching your application for the very first time otherwise when the application will create the tables MyISAM will be used as MySQL engine which is a non transactional engine that doesn't not support integrity constraints so even if later you swicth to InnoDB using an alter table all the integrity constraints would be missing as they would have been removed at table creation table by MyISAM.

MyISAM is not supported due to its lack of transaction support and integrity check, so use it only if you don't expect any support and if performances in read accesses are more important than the consistency in your use-case. Therefore the dialects mysql-myisam and mysql-myisam-utf8 are only dedicated to the community.

MySQL relies on collected statistics for keeping track of data distribution in tables and for optimizing join statements, but you can manually call 'ANALYZE' to update statistics if needed. For example

ANALYZE TABLE JCR_SITEM, JCR_SVALUE