I'm pretty sure the PlayCube was just made, sold, and discontinued.
So online stores can't just order more of them whenever they get a request for one, like they do with some items. You have to find a store that actually went and bought some of them while they were available.
However, when it first came out, all the pictures I saw of it in the reviews looked like this:
http://www3.telus.net/ragnar14/playcube-01.jpgWhen the GameBoy Player came out, a lot of people noticed that the PlayCube didn't work with it.
But then someone on these boards found a PlayCube, and it worked just fine.
Then I bumped into both the squared, purple one seen above, as well as this rounded, black one:
http://www3.telus.net/ragnar14/playcube-02.jpgThe black one works with the GameBoy Player.
I suspect that the black one was made more recently, although I'm not sure if it was specifically redesigned to work with the GBP.
So I think that sometime after the first PlayCube was discontinued, Nyko restarted, and then discontinued, another run of the PlayCube (and redesigned it too, while they were at it).