I've read reports saying the mortality was in the range of 30-40% for trout caught and released with bait. These were in raceway studies and my guess is that the rate would be somewhat less in fast flowing streams, since more fish would probably be lip hooked than deep hooked where there is current carrying the bait along.
But whatever the number, I do think it's probably true that the mortality rate is pretty high.
But this would be the case not just on the Little Juniata, but everywhere. If you apply such a rule on the Little J, why not apply it on all wild trout streams?
And let's not forget that on the great majority of streams the issue isn't deep hooking mortality on C&R bait fishing. On most streams you can harvest 5 per day.
Regarding the question of whether bait fishermen fish C&R areas. I'm not as familiar with the Little J as with Spring Creek. But on Spring Creek at least, bait fishing is very common, even though it's a C&R stream. You see more of it in the cold times of the year, and when the flows are up, than in low flow periods like now.
You see lots of bait fisherman in the cold months, from fall through winter and through early spring. Then in the summer not so many, except that they come out after a thunderstorm has brought the water back up.