"Whoever ... causes to be made unworkable or unusable ... any part ... used in connection with the operation of such aircraft, if such placing ... is likely to endanger the safety of any such aircraft"

The "part" is the PA system. While the device is playing the prank sound, it is temporarily "made unworkable" for its intended purpose of allowing the crew to communicate with the passangers. This "endangers the safety of the aircraft" because in certain situations it's possible the crew would need to communicate quickly with passangers or have silence so that they can understand each other and focus on solving an issue.

Edit: Looks like captain could override, flight attendants couldn't. That still causes a safety risk because in an emergency the cockpit might want to focus on flying the plane while the flight attendants instructed the passangers. Plus the distraction factor remains.