ZenCart has several types of emails that it sends out such as order confirmation, newsletter, welcome email, etc.

Each customer has a setting of "HTML email" or "Text email" depending on whether which they selected during signup. You can also alter the setting in the "Admin -> Customers".

If a customer receives the HTML email format, they will get a ZenCart logo with an alt tag of "logo". You want to change that logo image to your store's logo and set the appropriate alt tag in the email templates.

These email templates are in the folder...
email

The logo of the email is in ...
email/header.jpg

The disclaimer text is defined in ...
admin/includes/languages/english/email_extra.php.