Card counting is not illegal but using a device to count cards is. It's also interesting to point out that one of the members of the Nevada Gaming Control Board says that there hasn't been any reports of the program being used in Nevada. So, I suppose this warning is preemptive? I wonder which app got them worried?
Card Counter [iTunes link] teaches you how to count cards and its current description on iTunes almost takes credit for scaring the Nevada Gaming Control Board! Card Counting Practice [iTunes link] also teaches a card-counting technique.
But, the real culprit could be A Blackjack Card Counter [iTunes link]. It even has an "As Seen On CNN" banner. For most part though, all of these apps have a warning that using the app in a casino is illegal.