That low FPS seems highly unusual for your computer's specs. I'm with Minimurgle, it's probably the mods you're using. To be sure, try playing vanilla with a ship the same size & number of crew and see if you get much better FPS.
It is certainly true that Cosmoteer is far more CPU-hungry than GPU-hungry. Games like Fallout, Skyrim, and Subnautica are graphically-intensive games but use the CPU pretty lightly. Cosmoteer is the opposite in that the graphics are simple but it needs a lot of CPU to run the ship & crew simulations. The reason you see such a low CPU % is because that's a percentage of all your CPU cores (an i7 has 8 logical cores) and Cosmoteer isn't yet very good at utilizing all the cores. (There are some situations in which it can use multiple cores, such as running the crew simulation of each ship on a different core, but it's fairly limited right now.)
Turning off Animated Backgrounds won't help since that really only affects GPU usage which is not the problem. Turning off particles could in theory help but the impact is likely to be very small.