Reading Knopps book Giany clams and referring to page 99 uder the infection Rickettsia seems to be the closest thing to your description. The infest around the gills and systematically sit between bacteria and parasites. They say there is no cure or known treatment for this. They will infest the clams gills and kill the clam if the infestation get to large.
MAYBE, and this is a maybe a Mandarin Goby or a 6-line wrasse may eat them it the fish can see them.
Sorry I can't give you any more specific help but I hope this helps. BTW this Knopp Giant clam book is a great reference...
I hope this doesn't sound to incredibly stupid but could it just be new shell growth. I have no idea about your experience with clams so please dont take offense. Just a thought.
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