that hole is in the shell and called the byssal opening, the foot and byssal organ are usually located inside there. you can actual see the growth lines on the shell conforming to the shape. judging by the size and shape of that opening i would guess that is a crocea. the byssal opening varies depending on species and changes as the clam grows.
my best suggestion is keep on the snail patrol and possibly post a top down pic of the clams, there are many other tell tale signs that may help find any other problems.
HTH
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120S RR tank with 60G basement sump / fuge
Return Pump: Little Giant 4-MDQX SC
Water Movement: Seio 1500, (2) Hydor Koralia 4's
Lighting: 400W SE MH with 14K Aqua Connect
Skimmer: Euro-Reef RS250 with gate valve
Other: RODI, RDSB, PO4 / AC reactor
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