Apple's jailbreak detection API served as a means for device managers to easily check the status of their network's devices. The device managers would essentially ask the device if it was compromised, and it would alert the helpdesk, and exclude the potentially dangerous device from the Exchange Server.
This won't have much of an effect on the everyday iPhone user, but it will affect people using their iPhones as enterprise devices. MDMs, or Mobile Device Managers, won't be able to detect a jailbroken device. That jailbroken device could then unknowingly download malware, and put sensitive information at risk.
Jeremy Allen, the principal consultant with the Intrepidus Group security firm, explains that Apple's jailbreak detection was by no means foolproof: "It may be feasible to detect jailbreaks of a specific version or type, but they will still be trapped in the cat and mouse game they play with jailbreakers...it is a fairly intractable problem to solve 100%."
Maybe Apple recognized that their API was only providing a false sense of security, while jailbreakers were simply having to increase the frequency of their updates. In that case, perhaps device managers might prefer to use their own methods of detection, rather than a widely known API that is more easily circumvented.
source: Network World via Engadget