I just googled (not image search, just google) "Superman action figure". There were two pictures of old superman, and every other one was New 52 or Cavil Superman. Batman gives a bit of variety, with the New 52 mixed with a weird variant, one pre-New 52 Batman, and Nolan's Batman. So, they definitely merchandise New 52.
That said, a Harley Quinn search brings up a bunch of classic Harley and Arkham Game Harley, with only one New 52 Harley. Plus, the Lego Dimensions Harley Quinn is classic Harley, and the Lego Batman 3 video game also uses classic Harley (it looks like there is a pic of newer Harley as well, but that version isn't listed in character unlock guides or in any cutscenes). So, it looks like Classic Harley (with a bit of Arkham Harley) is still the go to version for stuff, at least when it comes to merchandise and games. Almost like she's the version people will pay to have..