Good questions. My experience with red autos and from observing red rental yaks is that after being in the sun for several years, the red tends to fade, or get kind of a washed-out appearance. However, in the case of autos, washing and waxing every 6 months or so will help prevent the fade. Also orange, and to some degree, yellow yaks experience the fade problem. I don't know for certain, but my educated guess is that this would be less of a problem with the sand (gray) yaks. Now there are wax-type treatments that can be applied to yak hulls to prevent or slow this, but not many folks use these to my knowledge. Also storing yaks under tarps outdoors or under cover (garage, porch) will prevent fading also.
In so far as the sand colored Mirage drive yaks being more prone to hull cracking, that seems to be a myth. It was mainly sand-colored OBs in a particular production run about 2 years ago that experienced this problem, to my knowledge. And you are correct--the sand will definitely be less visible on the water than a bright yellow, white, red, or orange one. The upside, if you are a hunter or stealth fisher, is that you would probbly be less visible to your prey as well.