It's not really about the airflow restriction. Especially in regards to filters; they won't restrict your fans much, if at all.
The key of cooling (well) is to ensure that you end up with as little noise as possible, for a good cooling solution.
Water cooling (if done properly) has the goals of (in priority order, highest to lowest): silence, performance, good looks. It is my view, that if you are doing water cooling, ALL THREE of these should be your priority. Silence CAN be sacrificed if you have a smaller case, or some other restriction, but to me, it defeats the point of water cooling in the first place. How do you achieve silence in a water cooled rig? By running fans which are specified for static pressure, and rated for silence at low speeds, and radiators to match (e.g. alphacool rads). This is something which the Corsair SP120 Quiet Edition are designed for. This way you minimise noise caused by airflow through the rad, while ensuring that the large number of fans in the rig are near silent (because they are spinning slower).
Air cooling: The priority changes for air cooling, since most non-stock air coolers are massive, and let's be honest, hideous to look at. The priority is: performance, price, specification to case (i.e. will it fit?). Note that looks and silence are not listed. This is not to say that you can't get a silent air cooled rig - you can, but you have to build specifically for that, and plan your airflow a lot more. Silence in an air cooled rig is a challenge, usually because the fans which go on the CPU heat sink, and the video card heat sink need to ramp up a bit higher to remove the heat from the case (along with the case fans), and this (generally) will cause more noise.
To directly answer your question; no, you should get some AF series (Quiet Edition fans) for your case, and use SP's only where necessary: on radiators if water cooling, or on your heat sink, if not. Placing SP's all through your case, will reduce your airflow potential at volt X (be it 5, 7 or 12), which in turn could reduce cooling potential through your entire rig.
Another thing to consider is: do you want your case to have positive case pressure or negative? Negative, will (generally) give you better temps, but it acts like a vacuum, sucking in dust all through the case. Positive will reduce dust intake significantly, but can (sometimes) cause slightly higher noise, as the internals of the case try and equalise pressure with the environment. The answer to this will determine whether you have more intakes than exhausts ultimately.
Edit: I've really got to stop dishing out novels in my thread replies. I'm so sorry everyone.