From what I've seen in my travels, vertical is dominant by far.  I think Texas is the only place I've seen where horizontal is common place.  However, some cities (Whitehorse, Yukon) may also use horizontal for their own signals.  I've also seen special cases (underpasses, low clearance areas) where they are used, even when vertical maybe the standard for the area.  Obviously red on top doesn't work for horizontal, so to making red stand out has to be done differently.  In Whitehorse, they use a larger signal for red than for the other colors.  In Texas, they use two reds side by side.  Yeah it maybe a little confusing the first time you see it, but you figure it out quickly.  The "Michigan left" took a little longer to figure out 

Usually, horizontal ones have, from left to right, red, amber, green, left green arrow (if used) and a second red. Furthermore, some have the red as a square, the amber as a diamond and the green as a round.

I've never had problems with understanding or getting used to them. This past summer, I noticed that Halifax, Nova Scotia (Canada) has some as well, but the vertical ones are by far more common.

I've never had problems with understanding or getting used to them.

The problem could be when you get glare from some awful sun position, then you become effectively color blind. Then the only recognition you have is the position of the light, Both color, as well as its shape become "unreadable"...