The Super Secret menu was enabled by pressing Control, Option/Alt, and Command keys simultaneously, clicking MacHeist Secret Stuff and entering your credentials into the resulting dialog box. These extra settings let you hide the app in the background, type anywhere to start a tweet and more. The latest version of Twitter for Mac disables this feature by preventing users from accessing the initial MacHeist Secret Stuff menu, at least by using the method listed above.
Twitter for Mac users that enabled the Super Secret menu will keep this feature, but new downloads lose the ability activate it using the above method. Though perhaps not desirable, the removal of the Super Secret menu was expected. When this hidden feature was first discovered, we wondered how Apple would respond. Thankfully, Twitter did not have to pull the app from the Mac App Store and was able to push out an update quickly.