The color only affects the cameras ability to pick up the laser. Green lasers appear brighter to the camera than red, but it isn't really an issue unless you are scanning very large items, or in bright ambient light conditions. Green lasers are significantly more expensive, and not really worth the cost.
With David-Scanner, I found the color didn't make as much difference as the intensity (power) and the ability to focus the laser into a very thin line.
Buy a decent, powerful, focusing red line laser on eBay, and you can get very clean scans with a decent camera.