I don't know exactly how many Pokemon have plushies, but I do that a good chunk of them can only be found at Pokemon stores. I think only the most popular ones/most marketed (such as Pikachu, Eevee and its evolutions, Riolu, and the starters of whatever generation is most recent) get plushies sold elsewhere. Another interesting trend I noticed is that certain plushies are more available during certain holidays: in my local Target I saw an influx of Ghost-type plushies on October (Gengar, Litwick, Phantump, Duskull, and Banette) for example. One that was over they conveniently vanished, though.