Yes, but after that the Super Mutants have been remodeled even further, just look at the screenshot of Marcus in front of Jacobstown. Marcus as well as the Super Mutant in the background now look very much like the original FO1&2 ones.
Well, I'd imagine Marcus has a unique model that is supposed to be closer to his original design, I'm not sure about the one in the background, though.
But if super mutants as a whole have gone through another design change, I'd assume that special types such as nightkin would too. It would seem pretty odd if generic mutants looked like the original Mariposa ones while special types still seemed closer to the Fallout 3 ones, after all.