I don't think there was - or is - ever a question of using the 16U2/ 32U2 unless you wanted HID (or other fancy USB) functionality or some exotic intermediate processing. It certainly is not a matter of cost.
That said, you have not described the context of your proposed project - few custom units or full production and sale; requirement for on-site or return-to-base (software) upgrade. If ICSP is only required for initial manufacture, you do not fit the pins - or even holes, but use the pads only and a "pogo pin" jig for that first burn. Which also applies to your main processor.