Shake well is an instruction commonly included on food products with liquid ingredients that easily separate into distinct layers based on ingredient density

Density

The mass density or density of a material is defined as its mass per unit volume. The symbol most often used for density is ρ . In some cases , density is also defined as its weight per unit volume; although, this quantity is more properly called specific weight...

. Consuming the product without shaking is usually not harmful but will result in dispensing only one part of the total ingredient mix, which may result in unusual flavors or food texture.

• Natural juices such as orange juice
  Orange juice
  Orange juice is a popular beverage made from oranges. It is made by extraction from the fresh fruit, by desiccation and subsequent reconstitution of dried juice, or by concentration of the juice and the subsequent addition of water to the concentrate...
  
   tend to contain pulp
  Juice vesicles
  The juice vesicles of a citrus fruit are the membranous content of the fruit’s endocarp. The vesicles contain the juice of the fruit. The pulp is usually removed from the juice by filtering it out...
  
   that separates from the liquid-only components, and must be shaken to distribute the pulp throughout the liquid.
• Oil and water products such as salad dressings tend to separate into two layers containing the water-soluble and oil-soluble components.

Homogenized

Homogenization (chemistry)

Homogenization or homogenisation is any of several processes used to make a chemical mixture the same throughout.-Definition:Homogenization is intensive blending of mutually related substances or groups of mutually related substances to form a constant of different insoluble phases to obtain a...

 milk is one of the few natural food products which would normally separate into layers, but the fats have been broken up into smaller sizes that form an emulsion

Emulsion

An emulsion is a mixture of two or more liquids that are normally immiscible . Emulsions are part of a more general class of two-phase systems of matter called colloids. Although the terms colloid and emulsion are sometimes used interchangeably, emulsion is used when both the dispersed and the...

that will not separate, hence the lack of a need to shake well.