Unos in final products have another problem besides the size. There are exceptions (I own a few of them), but generally they don't have solder holes or pads, so you're stuck with jumper wires which make for unreliable connections when left unattended. Or you can always desolder the female headers, but why do more work than necessary and alter a benchtop prototyping board that was doing its job?
The loss of USB is no big issue. You can use a little USB to TTL board or another arduino as a programmer. Do you plan very frequent updates of the product?