I will say that many of the motherboards I've bought have a stock cooler on the NB thats just barely above pointless.
But, I'll also say that water cooling a NB is as needed as watercooling a HDD.
What did the old Raptors and WD2000's put out heat wise? Around 8-12 watts, close to 20 on spin up. Isn't 8-12 the average for a NB? Maybe like 15-20 on a board or two on an extreme overclock? Will you get extra performance out of a HDD from watercooling it? No, but can you get more performance out of NB with water then air? Not thinking so. How about a Swiftech MCX159-CU (run passive) as some blocks will run about the same in price or even better, how about an old XP cooler run passively. How many still have these laying around? You might say it's too big to fit but we know thats not hard to get around. I've got a friend that was able to get one to fit under a graphics card using only a dremil to cut a row of blades out, a drill for mounting holes, and his fingers for fanning the rest of the blades out around his card (looks pretty cool).
He's not an engineer nor does he even have machining tools. Actually he did it in the college style dorms he lives in.
Bash if you like, but best I can tell watercooling a NB isn't really for cooling the NB. It's to look pretty.