USB chokes for USB power
My question is: will the additional CMC (on + and -) help with common
  mode noise reduction and will it interfere with USB signaling ?


Yes, but realize that the frequency cutoffs for USB filtering will be quite high at 700Mhz, so that still leaves a lot of room for lower frequency signals to get through the cabling. 

I would use a standard usb filter like the EMI2121, that way you know it's tested and you get EMI protection as well.

Another way to do this would be to use USB Isolation on each port and stop most of the noise from traveling down the cable, but this would add to the cost.