kill bill - Is the water mill when O-Ren and the Bride fight a homage to some movie scene?

Yes, it is possibly a homage.

This is extremely similar to the end of the opening "You brought 2 horses too many" shootout scene in "Once upon a time in the West" - right after the shootout, we see this turning, squeaking windmill.

I've managed to find a YouTube example. The relevant portion is between the 2:25 and 2:45 marks.

Please note that this is merely a possibility and purely my speculation, since I wasn't able to find that specific piece in any of the listings of homages, including those that list a couple of the ones from "Once upon a time in the West".