I think forage diversity is an important key to a healthy pond. Pay close attention to the little guys, and the big ones will thrive.
Having said that, we both know there are often unintended effects from adding or removing any species. For example, can clams be a parasite vector? As for phytoplankton depletion, I doubt that would be a problem unless your pond's bottom was densely covered with clams. If your water becomes too clear, you can always fertilize.
Interesting project CJ, and I hope you'll keep us posted.