One thing we need to remember is that the color of many crayfish is not a permanent condition. Often, there is both a genetic element and an environmental element at work. Environmental conditions can induce crayfish to display different color patterns.
Many of us have seen this when we have move crayfish or shrimp from one tank to another or when we've changed something like substrate, lighting, etc.
As an example, the professor I work with did some research on a species of crayfish which displayed different colorations in two different lakes. Crayfish which were captured from lake #1 and moved to lake #2 took on the coloration of those originating in lake #2.
Here is the abstract from his paper
Color Morphs of the Crayfish Orconectes virilis
Robert W. Thacker, Brian A. Hazlett, Laura A. Esman, Craig P. Stafford, Troy Keller
American Midland Naturalist, Vol. 129, No. 1 (Jan., 1993), pp. 182-199
doi:10.2307/2426447
Abstract
Adult Orconectes virilis exhibit a variety of colors from yellow to blue to dark brown that are strongly correlated with habitat background color. We used field and laboratory experiments to examine both the proximate mechanisms and the possible functions of this color variation among populations of crayfish in northern Michigan. Field transfer experiments showed that adults can change color, brown morphs becoming blue and vice versa. Light penetration measurements at six field sites indicated relationships between differential wavelength penetration and the colors exhibited by crayfish in a habitat. Holding crayfish in water from different habitats induced color changes while feeding crayfish vegetation characteristic of different habitats did not produce significant color differences. Laboratory predation experiments, field enclosure experiments, and transfer mark-recapture experiments did not indicate any differential survival of morphs that matched or contrasted with the background.
As another example, my home population of C. diminutus live in aquaria which has a dark black substrate. These crayfish are generally dark variations of grey, brown, and rust colors. A group of these which were moved to a tank with a white sand substrate have taken on a translucent and very light tan coloration over the past few months.
This will continue to make it difficult for us trying to select for specific colors because it is not always easy to distinguish between the genetic component and the environmental one.