Spoonbill are stocked every year. I don't think they can naturally reproduce in MO waters due to the dams. Essentially it is the same as catching and keeping trout from a park except they grow a lot bigger. A 100 pound spoonbill is a very old fish, but it's not like it was a wild fish to begin with. Killing a 100 pound spoonbill ain't like killing say a 100 pound catfish because that catfish will naturally reproduce millions of baby catfish. A paddlefish is just a big fish put for the pleasure of us to snag and it doesn't matter whether it's 20 pounds or 150 pounds as far as having an affect on the population of smaller spoonbill.
On a side note, I rarely keep spoonbill from the James anymore unless somebody wants one to eat. I just enjoy catching them. If I want some to eat for myself, I will keep them from the Osage below Bagnell Dam or from LoZ. The spoons from the James just have a funny taste to me unless they are smaller and have pure white meat, which I don't know until after I clean them. Most have a muddy looking meat though. I catch more big fish on the James though so that's why I keep coming back.