I know of one 13 inch Seacoast Mortar on the bottom off Holmes Beach in the Gulf of Mexico. The official records list the Maria Carlton as sunk in the Mississippi during the bombardment of the forts in April, 1862. Somebody got her back up and running as she is probably the vessel that dumped her mortar as she sank. Mortar and Schooner still on the bottom in close proximity to each other.
I haven't taken a count of existing 13 inch tubes. That would probably be easy compared to the non-existense of documentation regarding them during design, construction and operational use. Much disappeared from the National Archives.
Where in MA and CT are the tubes you mention located, Stephen? Are there plaques by the guns mentioning use or any names of personnel?