As long as you define your model associations properly, you should be ok. If you're worried about orphan records when deleting records, you can set 'dependent'=> true in your associations.

http://book.cakephp.org/view/1039/Associations-Linking-Models-Together#hasMany-1043

I'm using myISAM engine on my tables with cakePHP, had no problems so far =).

foreign keys are defined in model like this:

// this is a property of Post Model

    var $belongsTo = array(
    'PostCategory' => array(
        'className' => 'PostCategory',
        'foreignKey' => 'post_category_id',
        'conditions' => '',
        'fields' => '',
        'order' => ''
    )
);  

this means that current model is associated with PostCategory model using post_category_id column as a foreign key.