Using holes instead of vias for unused through-hole pins
If the connector you are talking about is what I think it is, then the "16 duplicate through-hole pins" are not duplicate pins at all - they are the B-side of the USB-C connector. Though in theory there should only be 12 of each.

Because it's a reversible connector, you will have two complete sets of pins, one set for the top side (the SMD pads), and one set for the bottom side (the pins). You must connect both sides up on your device, otherwise the connector will only work when both ends of the cable are plugged in in the correct orientation.