Okay, you cannot count colored cells, but what I do...........
When I am coloring them for a reason I will make the right column next to it with some sort of indicator......whether it be an x or a number....I will then hide it if need be.
I will then use my auto filter, grab the x and highlight the column.
In the right lower corner of your screen it should tell you how many you have highlighted......do you know about that feature?