From what I have learned about clams, most of the problems that occur are from lack of light.
Yes the fish can spook it. I have a maxi here and it was on the bottom as was yours.Although my tank is only 18" deep, it was shaded by other things and did not get enough light. When I moved it up to 6" below surface it has opened up more and it still has some way to go but I think it still needs more light.
Closing due to a shadow from anything is normal for these creatures. Thats how they avoid predators.
Holes in the foot could be a fungus or a predator from below.
Glad to see your clam doing better!