yes, if the clam is irritated by the fish constantly nipping and doesn't stay open. why do you assume it'll be a nipper if it hasn't yet? it could just be probing around the shell for worms or such, mine does that all the time. you'll have to hear from others on this but i think that if your cbbf isn't large it won't inflict mortal damage overnight, and may give up on the clam chowder, especially if the clam is firmly attached. keep your eye on it they may be o.k. together.
if it's of any help my cbbf which cleaned the tank of aiptasia and tube worms, eats frozen or freeze dried brine shrimp and small diced pieces of table shrimp. it also probe's the tank for worms and amphipods. hasn't touched the clams some of which were present before i got the cbbf five years ago. it was and still is about 4" and supposedly from the I.O. (not certain of that or if locale matters).