I've installed the new version of android 4.1.2 on my nexus 7. Now all my apps using the old c2dm system not getting any notifications at all.
Is there a need to change to the new gcm system to support cloud messaging on android 4.1.2 devices?
Short answer is YES.
Important: C2DM has been officially deprecated as of June 26, 2012. This means that C2DM has stopped accepting new users and quota requests. No new features will be added to C2DM. However, apps using C2DM will continue to work. Existing C2DM developers are encouraged to migrate to the new version of C2DM, called Google Cloud Messaging for Android (GCM). See the C2DM-to-GCM Migration document for more information. Developers must use GCM for new development.
see my answer how to integrate to GCM.