The way I like to connect my drives I/O up is have a short cable from the drive, shielded and preferably twisted pairs and have that going to breakout boards, you can then route from there to wherever they are going with the most suitable cable for the job. For encoders, analogue command etc I always use twisted pair, I have done some without shielding and it works fine but just short lengths and no where near anything noisy or mains voltage.
Hood