Well, Thunderbird's default format is to not apply any format at all other than what the user types in. Thus, if you type 1239998888 it will be stored like that. Conversely, if you type 123-999-8888 or (123) 999-8888 then this is how it will be stored in the Address Book.

Unless there is an extension/add-on for this, I see no way to enforce any specific formatting in the phone fields of the Address Book (and also keep in mind that formats differ among countries, thus there is no standard way how to do it).