I pitch the big roots and stems, and don't worry about the fine roots. When I prep the coco for re-use, I will screen it coarsely and remove the larger clumps of fine roots if there are any, rinse the fines out, and re-buffer with Cal Mag. This is for coco used indoor only, and that has not developed any pest problems.
For outdoor used stuff, or indoor stuff that had gnats or the like, I would re-use in an outdoor grow only unless I sterilized it first.