Some MyISAM tables not converted to InnoDB during 6 to 7 upgrade
It does make sense to convert all tables to InnoDB. The core 6 -> 7 update does not change the engine type; so the reason they weren't converted is that it was not programed to do so.

Use READ COMMITTED for MySQL transactions https://drupal.org/node/1650930#comment-8437127
Use 7.25 Core or higher https://drupal.org/node/937284

By doing both of these you will significantly reduce the number of deadlocks that occur on your database.

Using a non database cache backend like memcache is a good idea, as explained in this presentation: http://www.percona.com/resources/mysql-webinars/drupal-and-mysql-performance