It will surely vary with annual crop versus perennial crops. In most of perennial fruit crops, we measure flowering intensity as number of flowers per meter shot length...
I think measuring flowering capacity in seed/seedling stage is not possible. One has to wait until it flowers. Counting number of flowers in indeterminate growth plants is difficult, it requires periodical observations and flowers may not appear at every node. But, in case of determinate types, growth ceases with the initiation of flowering and flowering occurs at every node in basipetal manner.
As per my knowledge genetic markers will not tell us about the number of flowers a plant is expected to produce. If already markers are available, we can differentiate the flowering and non flowering types.
Expression profiling of the genes responsible for flowering may help in the quantification. But, the expression of genes is time specific and location specific. Hence, in seed/seedling stage it may not work.