Whether you go by the 4 sq. ft. minimum or the 2 sq. ft. minimum that I most often hear recommended, it means actual livable floor space. So anything that takes away from floor space should be deducted. Wall mounted nest boxes with usable space beneath would not take away from floor space.
If you're in an area that gets winters with snow/ice, I would highly recommend using the 4 sq. ft. min. But in areas that really don't get winters, 2 sq. ft is quite doable.
You will need to make sure your coop allows for enough linear roost space - 12" is recommended per LF bird.