The primary indicator used to assess the health of the stock is eggs. Other surveys are used more to assess the condition of the females, such as spawning conditions and the average number of eggs each female will lay in a given year. It is then possible to link the number of eggs to what we observe in the females. In my opinion, then, eggs are the most important indicator. I am not saying the others are not important. They are important too, but they are complementary.
As for how to fish for these fish, I must admit that, personally, I do not know enough to comment on the difference between the method prescribed by the Department of Fisheries and Oceans and what the fishermen propose.