I've never taken the top off of mine, but have seen plenty of them running around with no top and the wiper motor sticking up. I'd think you'd want to leave it on in case it rains...
Just got my first Bronco on Friday and it came with a bikini top with a spacer so it clears the wiper motor. I don't know if anyone offers that or if it was homemade but it sure is a good way to hide the motor while still getting the open air feel.