MySQL foreign keys add locks to referenced rows, and can have surprising effects on concurrent queries, particularly if you aren't running at read committed or lower isolation level.
InnoDB storage engine is available in 5.4, you don't have to use only MyISAM[1].
However, depending on your application, you may be enforcing these constraints elsewhere and not need them at the engine level, even if it's a nice-to-have.
There's also this: https://bugs.mysql.com/bug.php?id=48652 - still open after all these years (and yes I know there are much longer open bugs).