@jtreagan
I think its great you brought this subject up. No doubt, lots of fishermen feel the same way. These questions need to be asked, and they need to be answered again and again because the pressures that determine the quality of our fisheries is constantly changing - degradation of spawning grounds, water temperature, impact of commercial fishing, number of sport fishermen keeping or releasing fish, and so on.
Personally, I do a little bit of everything when it comes to how I fish. Powerbait, salmon eggs, worms for planted rainbows. Stinkbaits for catfish. Plugs, spinners and bait for salmon and steelhead. Plastic and plugs for bass. Flies and spinners for wild trout. Whatever method is legal on the water I'm fishing.
In college around 30 years ago I spent 3 months working on a paper analyzing data comparing death rate of trout when caught and released on bait versus flies. I am not a fisheries biologist, and that was thirty years ago, so I am relying on my memory. Though the details may have changed a bit over time, the end results should be close to the same today. Maybe one of you fishery biologists can chime in to correct and update anything I get wrong here.
Most trout caught and released using bait had a mortality rate of 40-60%. If they were throat hooked, bleeding or gut hooked mortality was much higher, sometimes approaching 96%. In those cases if the angler cut the line and did not even attempt to remove the hook survival rate was better. Between the effect of water and the fish's body fluids the hook barb/point dissolved in a matter of days and fell out.
Fly hooked fish death rates ranged from 2-10%. The range had to do with whether the fly fisherman was going barbless or barbed, and whether they were hooked in the throat or corner of the mouth. Fly hooked fish were usually in the corner of the mouth where they could be unhooked with the shortest and least traumatic amount of handling.
Data similar to what I found while researching for that paper combined with what was said in the posts before this one are reasonable explanations for why so many wild fisheries are fly and artificual lure only.
Waters managed for wild fish get fished out with bait faster than they can reproduce naturally. The same thing happens to wild fish if catch and release bait fishing is allowed. The death rate of released fish is higher than the reproduction rate of the few survivors. After a few seasons there would be hardly any fish left to catch. Of the few trout left most tend to be small ones.
Best of luck to you out there and tight lines, no matter what you're using to catch'em!