As noted by iLounge, Apple's Online Store is no longer offering the products online for shipping, but there are a limited number of cases and covers (in dark gray) that can be ordered for in store pickup. It is possible that retail stores may also have other colors as well, but the covers and cases for the older iPads can no longer be obtained online and will have a limited lifespan in stores too.
While it makes sense to discontinue the older varieties of Smart Cases and Covers to prevent customers from confusing them with the newer options developed for the iPad mini and the iPad Air, it is an odd move considering Apple still sells the iPad 2 to customers. The iPad 2 can only be used with a traditional Smart Cover or Smart Case, and is incompatible with the newly released iPad Air accessories.
Though Apple is no longer selling Smart Covers and Cases for the iPad 2 and other now-discontinued iPads, it does still list a number of third party options on its website. Currently, the remaining in-store Smart Cases are selling for $49, while the Smart Covers are available for $39.
Update: Apple is no longer listing the older Smart Covers as discontinued and is now offering them both in-store and shipped.