I love using this mod with fish as entities enabled, problem is though, they hog up the spawn cap considerably, is it possible to add a spawn rate thing into the config or turn down the spawn rates so they don't kill the spawn cap?

This is something that is controlled by vanilla, not aquaculture, sadly.

Aquaculture is is respecting the spawn caps.
It is caused by another mod - depends on what Minecraft version you are on.
Although make sure you are using the latest version of Aquaculture and Forge.