The practice long predates the existence of CRS, and goes back to when agents and others used printed listings like the Official Airlines Guide, where nonstop, followed by direct, flights received favored listings. CRS' merely perpetuated that system of showing flights. It's all about marketing...

AA used to have a flight that showed as direct SFO-ZRH, for example. Of course, we always landed at DFW, deplaned and boarded another aircraft (even when they were both 767-323ERs) for ZRH, and the award miles reflected the nonstop SFO-ZRH distance.