I'd would rather think it would be from a highly sophisticated amplification circuit, that would carefully monitor several microphones attached to the Hull of the ship.
Space, although largely being a vacuum, does have matter in it that can be used as a pseudo-media for sound waves to travel, although the speed at which sound travels would be greatly reduced to possibly cm or mm/s.
If shields are ion-based, then they themselves have a bit of matter, such as some form of gas or fluid. This means that if anything hit, or entered the shields, sound would travel much more quickly.