Part of tha board construction involved a wave soldering machine... for all the thru hole parts and that's when those holes were filled in. There are too many for any hand soldering.
Have they never heard of peelable solder mask?
And if I had designed the board with those pads, they would have been there so that you could implement RTS, CTS, and other modem handshaking signals, in the USB interface firmware.
The old FT232 chips they used to use provided them, but I don't know if they had them broken out into pads or not.