ATX and BTX standards assume a closed environment, will ventiliation being at specific points.
Moreover, with the case cover off there is no vacuum created by imbalanced fans. However, you are also rendering your case fans useless. They are simply moving air from directly outside the case - and right back out again. And, as mentioned above, having the case cover off exposes the computer to many potentially bad things such as liquids, flying objects, pets, fingers and more dust.
I would not suggest leaving the case cover off unless you had a fairly decent reason for doing so.