What changes does this plugin make that can break my site?
iThemes Security makes significant changes to your database and other site files which can be problematic for existing WordPress sites. Again, we strongly recommended making a complete backup of your site before using this plugin. While problems are rare, most support requests involve the failure to make a proper backup before installation. DISCLAIMER: Under no circumstances do we release this plugin with any warranty, implied or otherwise. We cannot be held responsible for any damage that might arise from the use of this plugin.
Note that renaming the wp-content directory will not update the path in existing content. Use this feature only on new sites or in a situation where you can easily update all existing links.