If you prune them past the green needles, you will have an ugly, dead branch. They do NOT regenerate green growth from the brown or un-leafed parts fo the limbs! (I have 30+ cryptomeria in my back yard and have learned a bit.) One arborist told me they “die from the inside out.” I think he meant they go grown from the inside out. So with sturdy gloves on, I have gently wiped off the dead needles from the interior branches of the tree. That has allowed more light in, removed the fire hazard of dry needles, and seems to have stimulated fresh growth in the green areas. From your pictures, I think you could do the same. If you want to fill in empty spots below, you can put in shade shrubs such as fatsia japonica.

cryptomeria