From what I understand, a heatpipe is hollowed in the center with some type of "wick" or aborbative lining. The hollow part is filled partly with a fluid and partly with vapor. The fluid is heated up and evaporates at the component load side and the difference in vapor pressure naturally forces the hot gas to the cooler end of the heat pipe. At the heatsink, heat is released through the fins and the hot gas condenses back into a liquid and is absorbed into the absorbative lining.
Here's where your issue comes in. Typically gravity will force the fluid back down the lining to the hot end of the heatpipe and the cycle will repeated. However, since gravity will not be working for you, capillary action will draw the fluid back to the hot end. It's like sticking half of a shoe lace into a glass of water. The water will start to "climb" up the shoe lace.
I say all that to say this - I think you'll be fine. You may forfeit a very small fraction of the HSF cooling performance, but I doubt it'd even be noticeable. So have at it!!
well heat moves upwards in direction if you are not blocking the flow of air then you should be fine. other people has already given info on the heatpipes