It is possible to add or remove an order tracking link in the order received email after a sales order is created.
Note: In order to have this feature Advanced Site Customization has to be provisioned in the account.
1. Navigate to Setup > Site Builder > Setup Web Site > Email tab > Customize Text Group Emails
2. Check/Un-check the Display Order Tracking Link
3. Based on the selection the order tracking link will or will not appear in the order received email.