Yes cyanobacteria can be different colors.Twillard, I have three different colors of thin mats on some of the rocks. All are in areas behind rocks where flow is a little lower (but not absent by any means). They are the typical dark red, an almost black color and a light green. All are thin and easily suctioned off the rocks. I had some of the red only in the sump which I resolved with turning the light off in the sump for about a week (no macroalgae there at the moment). No harm seems to be done by any of them although I've noticed the red stuff will show up on any damaged area of coral pretty quick.
Are there different colors of cyano and spirulina?
The typical is red then you have blue/green and then green.
You may have different shades of color depending on available light spectrum.