I don't know. Boring sponges bore into clams for habitat, not nutrition. However, the effects of their boring can indirectly kill clams by opening up entry ways for such nasties as predatory organisms. I'd be particularly worried about small clams. Larger clams, with thicker shells, will probably fare ok even if bored into; Most of these sponges only penetrate fractions of an inch.
If you wish to eradicate them, it shouldn't be too hard. Sponges aren't particularly hardy, and are easily "influenced" by environmental pressures. Indivudally injecting these colonies with hot freshwater will probably do the trick (hot kalkwasswer if necessary). If it hasn't spread to every region of the tank, removing the infected rock may be all that is needed.
Keep in mind that I'm not sure what species you have, nor do I know if it will bore into Tridacna shells. These guys may be harmless or harmful. For all I know, it might not be even a Cliona. I wish I could tell you, but sponges aren't my forte.
Curious .... Do you have SPS in your tank, or other stonies? Have they shown any negative symptoms?