I have the 36mm WoodCraft clip-on's on my ninja and it's a love/hate relationship.
Even without fairings these bikes don't really work with clip-on's. But that doesn't stop me because I love the low bars. Riding a stock Ninja 250 now just feels goofy. Lower bars completely change your riding experience. You get more front end feel. I love it. But then there are the negatives. You can't lock the wheel to the left because the bars smack the gas tank before stock full lock. It's only really annoying in slow tight riding situations. And trying to park the bike in certain situations. And you have to be careful that you don't hit the handlebars into the tank because you will either honk the horn or press the starter button while turning the bars. This makes you look like a complete idiot or ass depending on the situation. Haha.
Overall, I really enjoy the somewhat SS riding position but I'd have to say it's not really any more comfortable. Probably less. The bike just wasn't designed for clip-on's.