There shouldn't be any problems running it vertically. It's just the instructions stating for it to work optimally. It will still work fine in a vertical postion, with the air being blown back to the rear exhaust fan. My dad has basically a clone HS like that, and it has no problems with his E4300 OC at 2.7ghz.
The only reason why that perhaps state that, in what makes the heat pipes work better in a horizontal position, that the mechanism for it to work, has to do with the chemical in the heat pipes. So, it would work better when chemical is a liquid at the bottom of the heat pipe, then turns to vapor, which rises up, then cools back into a liquid to come back down the heat pipe.