While the show never specifically states that's what's going on, unstable molecules has been the canon comics explanation in Marvel for quite a while to explain away why, say, Mr Fantastic's costume stretches with him or how the Human Torch can burst into flame and his costume remain intact. They were in fact created by Reed Richards so he presumably either passed the tech around or has a heck of a patent on it.

Since Morph really is in their costume constantly in the show and shapeshifts to other forms with it on, I think that's more reasonable than assuming they're nude all the time (unlike Mystique who I believe really does go nude in the comics and is making all her own clothes when she shifts).