Yes, there are circumstances where a convertible top will make strange noises while driving and the top is up.
I have found that if the back window is closed (zipped up) and air is allowed to enter the inside of the car, either through the pull cable vents or the heater controls, and pressure builds up inside the car. This internal pressure increases with speed and pushes up on the top fabric. This pushing will stretch the top material and cause slack in the top material and it will flap or make noise as it flexes up and down against the top bows. This flapping is even more common and audible with the drivers window down. The pressure in the car has no where to go and pushes the top fabric up. The air flowing over the top on the outside tends to push the fabric back down and thus the flapping occurs. This flapping is usually not noticed if the back window is open (zipped down) allowing the pressure inside the car to escape and not build up.
I drive my convertible with the top down about 98% of the time so I have not experienced the problem often but I do remember it.
Hope this helps you.