Not only in articles
The core email cloaking plugin is a content plugin. This means it only works in articles and content that is specifically passed through the content plugins. As a result this often means that email addresses in modules and 3rd party extensions are not cloaked.
Email Protector is a system plugin and is written in a way that it will cloak email adresses in your entire website. So also in modules and 3rd party extensions.
Leave it like it is
The core email cloaking plugin has the option to convert all email addresses to mailto links or display them as plain text.
Email Protector has an extra (default) setting to leave the email addresses as you create them in the content. So if the email address is a mailto link, it leaves it as a link. And when it is only text, leave it like that.
Name: Email Protector
Version: Joomla 2.5, Joomla 3.x - 1.2.5