1st theory: She vanished into thin air, because she tried to leave Storybrooke. Bit far fetched, as none of the others who tried to leave vanished. There was just something pretending them not to leave.
2nd theory: She needed some air after she had the, well it wasn’t a crash (nothing seemed broken), whatever it was that stopped her, and she passed out or fell … If that is the case, I think the “real world” Frederick (Does he have a name yet?) went looking for her, found her and took her home.
3rd theory: She got out of the car (who wouldn’t do that after such a shock) and was taken by Sidney (or someone else. Don’t know, if he’d ever be up to that.) by orders of Regina. Kathryn is now held prisoner somewhere. The wooden hut? down in the hospital with Belle? Has Regina maybe taken her Heart now (Does she still have that power in the RW? We haven’t seen her [or Gold for that matter] do anything magical [except crushing Grahams Heart to dust].)?
P.S.: Sorry for all the parenthesis’. xD