While I agree that the separation of Lyropecten nodosus into two
species is questionable, studies of soft parts are not likely to
clarify such a situation.  Generally speaking, the internal anatomy
of closely related species shows less variation than the external
morphology.  You might expect this to be the case, if adaptation is
related to environmental pressures.  The external environment of a
species can change dramatically in a fairly short time (geologically
speaking), but the "internal environment", so to speak, is likely to
remain fairly constant.  Rhinoceros in Africa and tapirs in South
America are believed to have common ancestry, dating from when the
two continents were physically joined.  Externally, the two lines
have diverged morphologically, yet the two animals still have
identical intestinal protozoans.  The environments of the mammals
have changed over time, but the environments of the protozoans (the
internal anatomy of the mammals) have not.  Likewise, it is easy to
tell a fox from a coyote by external morphology, but you would be
hard pressed to separate the two based on internal anatomy, except
perhaps for minor skeletal differences.  But skeleton is analygous to
shell, and is not "internal anatomy" in the same sense that organs
are.  So, two species of Pecten may have fairly different shell
morphology, yet have essentially identical internal anatomy.  Either
you accept the separation into species based on shell morphology as
adequate, or you reject it as inadequate, but that is probably the
end of the story.
Paul Monfils
Rhode Island