Nigel,
This is a very technical and non-technical question at the same time. I would start by saying most people don't have room to hang them vertically. If your canopy is that tall then the rest of your lights are way too high. First of all I don't think it makes a difference, but if you want the long scientific answer here it is......
MH use a point source lighting system to create crests and troughs effects. This is maximized by two ways. One- having a direct point source, and Two having maximum photons. Some people would argue (probably correctly)that you could increase your photons and the brightness of the light by two ways. First of all put the light as close to the water as you can. That is the more important step.
The second way is to increase the "best" reflected light. This light is the light that is given off nearly directly upward and straight back down. You don't get as much of this when the light is vertical because the socket is above. Therefore people recommend mounting the light horizontally. Those who do mount them vertical (like seen in pet stores) often use a dome reflector to maximize reflection, but in personal tanks we don't have that option and use simple aluminum reflectors.
My opinion is that there is no reason to mount them vertically. But there are some reasons for mounting them horizontally (namely- keeping the canopy short and keeping lights near the tank).
Maybe someone else can share some ideas, these are just mine.
Adam
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