I've also never seen Emerald Crabs eat bubble algae. I recently put some in my frag tank and one rock that had green hair algae and bubble algae was stripped clean of the hair algae but they picked around the bubble algae. If it is just bubble algae you have then I would put a stiff piece of acrylic at the end of a syphon and get it out that way.
I know the theory is if you bust them trying to remove them then it will make more grow, but how can an Emerald Crab do it without busting them? Their mouths aren't big enough to eat them whole so as soon as the crab punctures them it will have the same effect.