I my opinion, bettas don't need aeration. I think you're right that it would upset them because their bubble nests would always be mangled up with the bubbles. Also, an aerator doesn't actually put much oxygen into the water itself, it mostly goes to the top of the tank anyway. Bettas are Labyrinth fish and just go up to the top of their tank and gulp air from the atmosphere.
Another reason against aerators is that if you don't have a heater in your tank or bowl, the water gets disturbed enough to release the warmth from the water.... think of hot soup and you keep stirring it or blowing on it to release the heat so that you can eat it quicker.