Right clicking on a material and selecting the objects with the material is how I'm selecting also, but that doesn't work right. It selects the hidden materials fine, but you can't change the material for those objects. So the current material stays on those objects and any changes you make only get made for the objects that are currently visible.
It's Really frustrating. I don't want to unhide all of those objects because they overlap and that makes it hard to see the changes I'm making.