I tend to think it's a disease, although I have no real evidence to back that up.
What I can tell you is that I've seen MANY squamosas and gigas in the wild that were big/old seemed to be otherwise perfectly healty - but had little permanently bleached patches here and there. That seems to rule out lack of nitrogen, food, and/or lighting as causes.
I don't know if it's an infection, or if there is some change in the system of tubes that holds the zooxanthellae, but either way, the good news is that this isn't rare by any means and as long as it doesn't begin to spread too much, the clam should be fine.
My 2 cents...