I noticed the reference planes generated by edited wall profiles return a Dimension element when using the method GetDependentElements, so they can be filtered out by that – oddly that method returns nothing on the reference planes auto-generated by railings though (not sure what other elements generate them as well). But in either case Revit returns an error when trying to delete those kinds of reference planes so they can be skipped.
Unfortunately that method doesn’t seem to return elements that are hosted on reference planes though (I was hopeful because it is a newer method), and those don’t cause an error when being deleted either. So I don’t really see a way to filter out reference planes that are hosting 
Deleting unnamed reference planes seems best practice to me - I usually name them if they’re going to host something anyway so they can be chosen from the Workplane list. The frozen node pictured from Archi-lab does just that