If all tables are myisam, should I use myisam engine instead of default innodb?
Software that uses MyISAM tables is often a sign that you are dealing with amateur quality software.  There have been very few valid reasons to use MyISAM for several years, now... ACID and intelligent crash recovery and foreign key constraints are just a few things that come to mind that MyISAM will never dream of being able to provide.

Turning off InnoDB because you aren't using it is also an exercise in futility and short-sighted at best.  It is essentially just tinkering with your server for no good reason.  Leave that setting, and virtually all of the other settings, at their default values unless you have a specific reason to change them.  Tweaking parameters requires discipline and deliberate, well-informed action.

Oracle has officially deprecated the ability to do this, anyway.  As of now, in 5.6.23, disabling InnoDB still works, but results in a warning that it is a capability that will subsequently be removed... which should tell you something about whether it's a good idea.
http://dev.mysql.com/doc/refman/5.6/en/innodb-turning-off.html