Coming to this game after having played I, II, III and IV, it took me a while to wrap my head around what granaries and water mills now do and why that matters strategically. I generally agree with the importance of workers, but everything is map dependent. You can prep are the tiles you want, but if you are too low in population to work them, it takes a while for that to pay off. With water mills, you get extra production and food for only the price of maintenance and the hammers. In fact, if you are swimming in gold but not hammers, it could make sense to buy a water mill in a city that needs a jump start.
In answer to the original question, I see three reasonable choices for water mills in each city:
1) A water mill in this city will not sufficiently offset the cost in gold or hammers and/or maintenance.
2) A water mill in this city will be useful, but can be prioritized low.
3) This city was located where it is for reasons other than food. It will be OK once it grows a bit, but it needs a water mill asap to boost population and hammers. I can afford the maintenance cost. I'll either build it or buy it as soon as possible in this city.