I think you will want to go with the fluorescent tubes due to the heat build-up and clearance. You could use the externally ballasted mercury vapors but the bulbs are still going to be pretty long and I'm not sure how much cooler they run, but they're probably better if you're stacking and/or mounting inside.
I'm using self balasted mercury vapors in cages with 18" height. The lights are in domes which are recessed approximately 4" down into the tops with extra space around the edges to let heat out. My enclosures are built out of 1/4" thick hard ply and still run pretty warm. The only thing that lets most of the heat out is the half front doors I use that leave it open across the top in the front. The last one I built with sliding doors ended up putting the vents in the top instead of the back, it works much better. I kept drilling 2" holes until it reached a good temp range.
Even still, its up to personal preference. If it doesn't really matter to you, the tubes will make it easier. If you kind of prefer to go with mvb's, you'll work around it until you find out the best way to set it up. Once it's done you'll be good to go. I like using the mvb's, thats why I did what I did, although, I'll probably be drilling more holes come summer time.
Another thought, if you like mvb's, you'll probably try all the different ones until you find one you like best. Some run cooler, some hotter. At least if you go with a fluorescent tube, there's only one real choice there for brand.
Sorry if this is so scattered and undecisive, hope my experience with mvb's and heat helps your decision. I know it would have been so much easier to go with tubes for me.