This is because Apple requires that any application that is distributed via the App Store is sandboxed. This is perfect for casual games, as it restricts the level of access that an application has to parts of the operating system. However, for an advanced tool like CCleaner for Mac, it's a major headache.
So, following this Apple requirement that was introduced in July 2012, we will sadly, no longer be distributing via the App Store.
You can download the latest version of CCleaner for Mac from http://www.piriform.com/mac/ccleaner