If you look at it from a space perspective, an mtb takes up roughly 7ft x 3ft x 4ft (LxWxH) of space. So for people with limited free floor space, the question is how to cram as many bikes as possible into that space while still having any one bike accessible. Stacking them horizontally and back to front against a wall you could fit four bikes into that space - two on the floor and two above hanging on hooks of some sort. But that means you have to move two bikes if you want the one at the back. If you hang them vertically, you can get maybe three bikes into that similar space, but it means they project out into the room an extra foot as opposed to them standing horizontally and leaning against the wall. The advantage with vertical is that any one bike is a bit easier to access. So barring cost, bike storage is a compromise between taking up space and ease of access. I only spew all the obvious out as I've grappled with chaos for a while as I have multiple bikes in a perpetual state of floating all over the place and moving around to accommodate a few different things.
I think if you only have two bikes then stacking them up against wall with hooks/shelves above for gear, tools etc works really well. If you have three or four bikes then the same with two on the floor and two above and you can still have some space to hang gear. If you get above four then it gets trick. I'd guess it probably makes more sense to go vertical and alternate the height of the hooks to get them close together. Or if you have more space then you could do another horizontal stack somewhere else. I'm still holding out hope of finding a sugar momma so I can have a 1000sqft shop to store all the bikes, tools etc. and not worry about having bikes and gear in the dining room, living room, hallway and spare bedroom.