I think the concern that the /audio/ of the machine will reveal the contents is nearly absurd. The bigger risk is the networking of such machines. I think this falls under the general risks associated with the general "Internet of Things" (IoT) that we're seeing developed more and more.
For that matter, how many CNC machining centers are networked to an internet-facing server? 3D Printers aren't the only thing vulnerable. There are many machines that are deliberately internet-facing so that supervisors can monitor in/efficiency, operators/machinists can be notified of downtime (our EDM machines can send a notification to the wire EDM machinist that there's been an alarm, so he can come in and check it out), or because there are 3rd party software or services requiring internet connection to monitor/collect data.
It's one of those security concerns that mostly falls under the "security through obscurity" umbrella. Who's going to hit that vulnerability? What's the likelihood? Anyone who needs the level of security will have secure networks that maintain an air gap.
I have doubts about just how well one could duplicate the model being printed though.
"Using this technique, Al Faruque and his team were able to reproduce a key-shaped object with almost 90 percent accuracy."
"90% accuracy" doesn't tell me a whole lot. And the devil may be in those details.
However, how would one conduct such espionage in the first place? If they are able to record the sound of the motors, why would they not have a more practical means of duplication?