Personally....I would not have used a broad spectrum herbicide (fluridone) to treat such a small area of duckweed. (1/2 gallon of Tribune at around $25-$30 would have worked fine) Unless you were very accurate with the dosing, the fluridone most likely was affecting other aquatic plants as well. Shallow water = organic rich (sapropelic) muck with EXTREMELY high BOD.
I believe that an oxygen meter is EXTREMELY valuable in these situations. Everything else is guessing and theoretical calculations that mean nothing to a dying fish from lack of oxygen. Inadequate aeration in a organic bottom rich shallow pond can be more deadly than a pond that is not being mixed with artificial aeration.
Very sad to read that such a healthy fish population has been eliminated with good intentions.