I don't see any problem with having one or two shakes a day. The problem comes when people think they can rely on shakes for all their meals. The benefits of whole foods is that it speeds up your metabolism as your body has to expend more energy to break down the food when compared to a shake.

For the nutrients question, I believe your body will absorb the nutrients the same but with a shake it will be a much quicker process while the whole foods will take longer to break down and lead to a slower controlled nutrient release.