Capture Net VS gathering/fishing

The capture net is mainly used for endemic life. Bugs you can just go up and grab now, much quicker and reliable than deploying the net. As for fishing, sure you can use the net... but as you pointed out, this scares and scatters the fish whereas the fishing pole does not. The capture net also cannot use bait if you want to be going for specific kinds of fish.

Use the net if you want endemic life, your hands if you want bugs, the pole if you want to fish.

there is no loot table as you know what your getting when you see it (the scout flies tell you), and once you fish enough you'll just recognize what they are... no loot tables involved with gathering life (bonepiles and mining points and such still use a loot table)