I believe you are speaking of the "Email Notification" that you, as the form Author recieve, which is setup on the "Email Notifications" sub-tab of the "Options" tab. In that email notification there is not an option to hide the blank fields. In the "Email Reciepts" sub-tab of the Options tab is where you configure email receipts sent to the form submitter, on that tab you can choose to incude the data but hide the blank responses, but that does not affect the email notification that you, as the author recieve. That email notification, if you choose to include the data, will always show all fields.
Let me know if that was not correct and you are saying that the email reciept to the submitter is showing blank fields when it should not.