If the case has super cooling otherwise, the difference might indeed not exist or even be negative. But if the case has less cooling, then the fact the water cooler pushes the heat right out of the case ought to make a difference. At least according to my own experience. I have the same water cooler model in my current build that I also had in my previous build, although the CPU is different. The case isn't much different, basically just a slightly updated model. However, the previous build had all the fans from my pre-water cooler days, whereas this current one has reduced fans. There are no heat problems, which I largely credit to the water cooling not leaving the CPU's heat hanging inside the case.

As we all know, Bill likes to bake bread inside his computer case (that is, keep is as hot as the components can stand), so I could see water cooling being an option. At the same time I have to note that you should choose the cooler carefully, because they do produce distinct sound. Unfortunately, I guess due to liquid circulating inside a closed loop (unless you build a real custom water cooling), the noise can be uneven and most of all it varies between the individual coolers. So, when you get your cooler, if luck favours you, it might be very nicely silent, but if you haven't sacrificed enough at Fortuna's altar, you might get one with strange extra noise. My luck wasn't perfect. But then again, I didn't even study the models of different manufacturers too much, which probably was a mistake.