Earlier today, a report from TUAW's Erica Sadun suggested Apple would be banning apps from the Mac App Store that use any global hotkeys. Fear not, Alfred and Skitch fans: according to both MacWorld and our own sources familiar with the matter, this is something of a misunderstanding and those global hotkey-enabled apps should be fine.
The original story cites a known June 1st deadline for developers to ensure their Mac App Store apps meet the new sandbox requirements, that restricts some of the system and user permissions. (Microsoft has has a similar sandbox initiative for Windows 8 Metro apps.) We've been told that registering global hotkeys is still covered by this sandbox API, which means for example you should still be able to set a keyboard shortcut that pulls up an app or, for some Twitter applications, immediately jump into a New Tweet window.

Source: Mac OS X Developer Library
What is prohibited from the sandbox API is the ability for apps to keylog or track all your input in an effort to avoid potential malware — an app can't simply listen to every single keystroke coming from the keyboard. We've also spoken with several OS X developers who sell through the Mac App Store, none of whom seem concerned. A couple additionally cited Developer ID and Gatekeeper, which allows a second tier of security and lets apps that work outside the sandbox API to run just fine, provided the ID is registered to a known developer — only difference is those can't be sold at the Mac App Store. So in either case, whether or not you update to 10.8 Mountain Lion later this year, your current OS X apps setup isn't going away.
Chris2 — that is, Chris Welch and Chris Ziegler — contributed to this report.