I know it's Ars, but there has to be a better link with more detail than "here's a thing some people might be doing, somewhere."
Take a look at Chirp: http://www.chirp.io/ Edit: In Firefox it seems this website is constantly playing audio. I think it is using a WebSocket to do this. Since I don't hear a thing I'm not sure what is going on here.
Click on the gem and the web page will play a "chirp," which is loud and beepy and not ultrasonic or secret at all. It's an analog modem type system, except probably way slower than 300 or even 110 baud. Everything old is new again, I guess.
In any case, the point is: the Chirp system is distinct from the supposedly-possible secret systems the Ars story is fretting over.
I've seen several articles worrying about the use and abuse of data transmission via secret ultrasound, but I've never seen any claims that named names or that offered a way for readers to verify or check anything.
I don't think you can count on the average laptop/phone speakers, mics, and digital audio systems to deal with ultrasound.
If a computer's audio drivers and audio hardware are set up to play back at standard CD/DVD sample rates (44KHz or 48KHz), then ultrasonics are not happening there, period. The same principle applies to inputs.
Even if all the hardware and software on two devices is capable of and configured for producing/receiving ultrasonic frequencies, it seems pretty likely that loud ultrasonic screeches played on a 50-cent cell-phone speaker would produce audible harmonics, and the jig would be up.
I expect secret ultrasonic data transmission over commodity systems is the sort of thing a well funded state organization might turn to for a targeted operation. Because it might work under exactly the right circumstances, but it would be fiddly and terrible for general use.