A remote introduces additional contacts and active electronics (if it has a display), which may affect sound quality, so it is obviously better not to use it. The cleaner the path, the better the sound.
The clamp filters do not affect sound quality in any way, and are totally useless in a normally working system. Their only function is to prevent the respective cable from becoming a radio noise transmitting antenna in case your computer turns mad and starts outputting radio frequency signals from its USB port. Such things do happen, and may affect entertainment/traffic and equipment control/emergency service radio transmissions in the neighborhood, but the probablity is infinitesimally small.