The scientific methods for counting red snapper (I have performed this research) are outdated and inadequate. Problem is, there is 20 years of poor data. If you come up with a new method for determining the population of a fish, you throw all that came before it away. That's millions and millions of bad research down the drain, so instead, we keep collecting more bad data.
Specifically, red snapper are counted by trapping them. Problem with trapping them is that the traps are on the bottom (for 40-50 minutes) and the red snapper are distributed throughout the water column. Second problem is that no matter how many sow red snapper are in the vicinity of the trap, only one (and rarely 2) will get in the trap together, so the trap may have a hundred snapper looking in at the menhaden bait (Menhaden is the only bait used), only one is gorging itself.
Now, many little reds will enter the trap with the sow, so the scientist sees (when the trap is hauled) one "keeper" and a ton of fingerling. What does that tell you? I'll tell you what it tells you, it tells you that there are a bunch of young snapper out there, but very few big snapper.
Now, I'm just a dumb research boat captain, I would never tell the NMFS scientists that their methods are wrong, right? Well, lets just say that after that one trapping trip, I wasn't asked to do any more. Especially after seeing a ton of dead and dying snapper thrown back, and poor scientific methods, and general mayhem on the deck, I couldn't keep my mouth shut (Shocking, I know). Ask any charter fisherman how the snapper are doing, they will tell you they are flourishing.
But a scientist told me that Red Snapper are functionally extinct in the Atlantic.