I believe that if you have the 'Remember form settings' option enabled in the Company Profile, then the most recently selected email cover will be defaulted the next time a document is printed (or emailed).

There isn't a generic place to set a default email cover for the whole company.

You can set default email covers directly on the customer, though to use these, you have to email OE documents using the 'Use Customer Specification' option.

If there is no email cover on invoices found in the email queue, then the cover field was blank at the time of emailing - an email cover was not selected.