Various fungi, algae, bacteria, etc. have some capacity to make holes
in calcium carbonate.  Either acid or various enzymes could etch the
shell.  Might the culprit be something in that line?

It would be useful to know the exact shape of the entire burrow to see
if there's anything diagnostic.  This generally requires filling it
with something (resin, latex, etc.) and pulling it out or dissolving
away the shell.

--
Dr. David Campbell
425 Scientific Collections
University of Alabama
"I think of my happy condition, surrounded by acres of clams"

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