Night owl coder here. It comes with the job I think, our job is creative and our minds toy with us to no end.

I have found I can "cut off" the deep thoughts by writing them down. I keep a notebook next to my bed and if I can't fall asleep because of something I want to program, I will write out everything about it in the notebook. After that, I'm far more relaxed because I am not worried about losing the knowledge once I fall asleep.