Square ships iPads, most of the other payment terminals are some brand of leenucks (some are android, some are not.) There are more WinCE terminals still out there than you would expect (verifone's been around for a LONG time and has probably used every embedded toolchain/cpu architecture/rtos that's come down the pike. And that's just one example.)
IBM 4690's supposedly run a SuSe derivative, and Walmart doesn't seem to be replacing them with iPads. I think Sears & KMart also used 4690s, but also a mix of predecessor systems which ran an unholy assemblage of OSes: flex, dos, a bizarre mix of Os/36 and IMS, etc. As best I can tell, they never ran an OS from CMU.
Next time you're in a gas station, grocery store, cinema or chain restaurant look closely at the cash register. It's not an iPad.
Square did a mightily brilliant thing to marry its dongle to a consumer friendly iPad to support small retail, but apple is not in the business of selling PoS systems. Heck, apple stores didn't use apple devices for PoS for the first two or three years after they were launched.
The assertion that iPads are "taking over" PoS seems to be based on an inappropriately small sample.