"As usual, Instapaper 3.0 is a free upgrade to anyone who has ever bought the paid app. For new customers, it’s only $4.99 for the universal iPhone and iPad app."

If you search for Instapaper and re-download you'll get 3.0.

It seems that the updates section has a little bit of a delay.

Probably hasn't propagated yet. It'll take an hour or two most likely.