It looks like with the impending release of Apple's mobile OS, iOS 6, that we could see a change in the podcasts section of Apple. Sources have revealed to AllThingsD that Apple are planning to release a native app that focuses solely on podcasts.
iOS 6 is said to have a dedicated podcasts app, which will let users discover, downloads and play podcasts on mobile devices. This is a similar move Apple played when they decided to split iTunes into a video and music app on iOS, as well as launching the iBooks app with the iPad release.
If this ends up happening, it may explain the disappearance of podcasts from the version of iTunes that Apple has been showing off to developers.