Q1 / Q2
Equirectangular and “mirror ball” bascially represent two ways of creating a HDR environment map. Mirror ball is easier to create, as you “just” have to take a photograph of a… well… mirror ball, while creating a full 360 degree equirectangular map would require taking a significant number of photographs and stitching them together afterwards. So the latter eventually is more expensive (equipment) and time consuming if you want to do it right.
As far as using them in your scene is concerned, a mirror ball map will be good enough for CG lighting and reflections in most cases. Only drawback is that it’s usually too low-res (and perhaps too distorted) for backdrops. So, you could say that a very high-res equirectangular map is most versatile, as it can be used for lighting, reflections and as a background image. The file size will be gargantuan, though.
As for the “black below the horizon line” thing: In many scenes you won’t see anything of the environment map below the horizon anyway, as you have a 3D ground plane in your scene. So, why not turn the ground area of the environment black in order to save on memory usage?
There is no difference in ease of use between the different types of maps. Only thing you have to remember is to select the correct projection type (Equirectangular / Mirror Ball) in the Environment Texture node:

Q3
Theoretically OpenEXR should be the superior file format in terms of color fidelity AFAIK. But then again, this doesn’t really matter for HDR images you want to use as environment maps. In that regard those are just different file formats to represent (more or less) exactly the same data.