Out of curiosity, I googled "how to farm clams." Here's one site:
https://thefishsite.com/articles/cultured-aquaculture-species-northern-quahog
Clam farmers have some legitimate concerns. One stage in the farming process has the clams in mesh bags or covered by mesh to prevent predatory losses from lobsters, crabs, and other hungry creatures. Anchoring committee boats or marks could damage the mesh or bags and cause losses to the farmer. However, just sailing over the beds should not cause a problem.
Areas with active beds should be marked so sailors, fishermen, and casual boaters do not anchor in those waters. however, blocking navigation over the beds seems to be a step too far.
Time to begin lobbying the decision makers. Contacting BoatUS seems to be good idea.
One question to ask is how the plots will be leased, is a random assignment? Are there more desirable lots? Can the areas that clubs use to race be the last to be leased? Perhaps a club could get a lease for the areas where the club races, first boat across the line each week has to harvest clams for the rest of the fleet?