I've spent too much time reading about what happened today, but my conclusion is that there was a mixup with the online order system which confused absolutely everyone, employees included, by allowing the Pencil to be ordered for store pickup even though the stock hadn't arrived.
The actual in-store launch is still "later this week," which is why stores were turning away walk-ins and many had not set up their demos properly. The confusion was that people who saw availability for in-store pickup assumed this meant the in-store launch was happening today. Some people had also seen in-store availability for the Pencil/keyboard, so we concluded that accessories were in such short supply that they had sold out instantly. In reality they weren't supposed to sell accessories at all, and any Pencils sold were an error (one guy got a box labeled something like "demo unit do not sell").
The point is that if this is correct then it should be possible to get a Pencil on Friday (or Thursday? I'm just going off the original 11th, 13th rumor) if you get there early. Today's availability was not a representation of the stock they'll have available. They should have a second batch of IPP units for walk-in purchase as well.
*edit: cleaned up. Believe it or not this is the more readable version of the post. Also to add that while it makes sense in retrospect, having in-store pickup availability without an in-store launch is confusing even if it's intentional, unless you explain it that way. Also++ the online stock suggests that Pencil may still be limited, I'm just saying they'll have more than 2.