Everthing sent over the wire including cookies is encrypted if using ssl. Even when not using ssl, nothing sensitive is stored in the cookie itself, its just an authentication token. The value in stealing it is not related to its contents but in the possibility of spoofing a priveleged user if you could convince the server that you are that user because you have that cookie. Passwords are never stored in the cookie for example.
In mojoportal, if SSL is available it will automatically use it on login, register, profile pages, but you can also specify to use it on all pages or on a per page basis depending on the nature of your content on those pages and whether it is sensitive data, you may want to use SSL on additional pages.
Hope it helps,
Joe