In short, Blizzard really did vastly underestimate just how popular these authenticators would be. Not only were they unable to deliver as many as needed, but many areas, including most of the non-US world, were unable to order them. With these unexplained refunds, and no announced ETA for the Authenticator to become available again, it seems like Blizzard really has been blindsided, and may still be scrambling to get on top of this glut of demand.
It seems strange that they really didn't understand how popular this world be. Almost every day, a new glut of key logger posts from stolen accounts show up on the official forums, as hackers and gold sellers work overtime to steal new revenue sources. Everyone seems to know someone who's been hacked. No matter who you are or how you play, you're vulnerable. Even if you aren't hacked directly, you may still feel the sting if a fellow guild member gets hacked and your guild bank gets cleaned out. With that type of craziness going on, it's no wonder more people are looking for more ways to keep their accounts safe.
Perhaps this is just another example of what Rob Pardo said at the Paris GDC: Blizzard approached the MMO game rather naively. This naivete may be what keeps them from providing the security their customers need. Of course, they aren't under any obligation to provide more extreme measures like the Authenticator per se, but they understand very well that the things account stealers do damage the game as a whole. In that case, it seems like they should have been more prepared for this.
Hopefully, Blizzard can recover from this setback quickly, and get back on track for selling more Authenticators and making them available to players everywhere. While it's good to see Blizzard help players take action against account theft, it only works if the help is consistent, universal, and readily available.