This is a very broad question, and depends on your perspective. As a researcher with some experience in hatcheries, I often consider progress in terms of percentage success and this can be broken down in to specific production phases (spawning, larval rearing, nursery). In the case of bivalves, this could be the average fecundity of broodstock, the % of eggs that develop to D-veliger, the % of larvae that reach settlement or the perhaps % metamorphosis. For commercial hatcheries the evaluation could be based on the cost associated with each production phase, or perhaps the final cost of production per spat or fingerling at sale size (both of these can account for improvements in the rate of development or growth, that may not increase the percentage success, but reduce the time taken and the cost associated). There are lots of examples of these metrics in the aquaculture literature. Depending on the use of the spat or fingerlings, their health or robustness might be considered, as could the genetic diversity of the batch if they were destined for activities such as restocking.

FCR or Condition Index are few good indicators

Productivity can be measured in many ways. If you refer productivity as a measure of feasibility of the venture you could refer to the production data and compute for ROI, break even quantity/price etc. While if what you are telling on productivity in terms of biological performance of the organisms being produce then look into the data for survival/mortality rate, growth rate, condition factor and other indexes .