This isn't an easy option for XenForo. You can edit the email logo in the
style property settings, but this only applies to
Activity Summary Emails.
If you want your logo to appear in emails received for direct messages, you have no other setting that makes this possible.
Fortunately, we can edit templates.
Go to
Templates => MAIL_CONTAINER
Find the following lines: (should be on line 19)
Code:
<a href="{{ link('canonical:index')...