For one thing, clarity will help determine the particulate content of a fluid. This doesn't help as much for nanoscale particles, which do not scatter light as well as bigger particles do. So, while apple just may be clear and therefore superficially "homogeneous", there may be (probably are) still particulates in it that you just can't see.
In scientific analysis, "eyes" aren't the greatest instruments. There are better analytical methods to determine particulate content, like DLS.