The count isn't the number of unread emails, it's the number of notifications sent to the screen by the email app. If you have notifications turned off in the email app, you won't get anything on the icon. If you swipe the notifications away you won't see anything on the icon.
Nova shows the actual number of emails (missed phone calls, unread texts, etc - whatever apps you have badges turned on for), so notification or not, you get a number if you have unread emails.