It probably doesn't make much difference, but I suspect it also depends on your application. If your joint must withstand more shearing force, I would expect the smooth dowels to be slightly stronger at resisting shearing, all else being equal. If you have a single dowel that must withstand rotational force (such as in a knob), maybe a grooved dowel is better (like treaded vs. bald tires). If the joint must withstand pulling or racking force along the length of the dowel, there may not be much difference at all, but I would somewhat expect the grooved dowel joint to be weaker since glue on its own is not a good filler and the insides of the grooves are just open space with no mating surfaces.
I've always thought the grooved dowels were simply designed to be easier to push in. The grooves provide reduced contact area between the dowel and the walls of the hole, and at the same time they provide channels for any excess glue if you didn't drill the hole slightly deeper than the dowel. This also means you won't get an air-tight seal that causes compressed air and/or glue to push dowel back outward.
On the other hand, perhaps the grooved dowels are slightly oversized, and they deform inside the holes so they remain compressed and tight-fitting at all times. But you could just as easily make a tight fit using a smooth dowel.