We've heard it through the grape vine that Apple is preparing to do away with apps that include hotkey shortcuts in the Mac App Store. Sources say that apps submitted before June 1 will only be allowed to receive updated pertaining to bug fixes while any new apps or added features cannot contain hotkey support.
TUAW points out that in-app hotkeys and macro programs in general can be used to accomplish a number of tasks, including but not limited to bringing specific features to the foreground inside a program and even launch all of a user's most-used apps simultaneously. I use macros on a daily basis with my Logitech G510 keyboard and can attest to their usefulness and time-saving attribute.
The problem, as Apple sees it, is that hotkeys, macros and the like could potentially be a security risk. These features are typically only utilized by power users, a demographic that Apple knows won't pay dividends down the road. iOS' simplicity and strong security is the future and a proven money source for the company.
Apple has built a sandbox with iOS and those claiming to be in the know say the same level of scrutiny is coming to the next version of OS X. Do note that the hotkey restrictions currently only apply to Mac App Store purchases and there's not yet any indication that Apple plans to try and restrict the sale of hotkey-enabled apps outside of their ecosystem.