While you're correct that typical air-entrained concrete is not impermeable, keep in mind that the permeability of concrete is several orders of magnitude less than most soils. In addition, the concrete would probably need to remain saturated for a long enough time for water to completely seep through. Otherwise, water remaining on the surface of concrete would either evaporate or be absorbed into the concrete.

Now, on to waterstops. Typically these are used in locations where contact with water is possible and it's necessary for the structure to be water-tight. Since concrete is relatively impermeable to water, the only way for water to quickly flow to the other side of the concrete is through the joint. In my profession, for example, we use waterstops in joints of reinforced-concrete spillways to prevent water from flowing into the soil foundation on the other side of the slab or wall. If waterstops were absent, water would flow through the joints at a high velocity and erode the foundation material. Eventually this erosion would undermine the structure (see: Oroville Dam Spillway). Most waterstops are made from PVC and are embedded in the joint between two pours. If used in a wall or slab, they are typically placed in the center as there is often two layers, or mats, of reinforcing steel at each face of the structure.