Don't worry i have a workaround to trick cydia from updated notification for all those cracked apps :
1. Using iFile, navigate to /private/var/lib/dpkg/
2. Make a backup of file "status"
3. Open the file "status" using iFile Text Viewer
4. Find the package that Cydia is asking you to update.
5. Change the version number to the new version number of to a higher number (hit the Edit button in the iFile Text Viewer).
6. Save the changes and restart Cydia then you can see the notification is removed.
If you would like to receive update notification of certain apps again, just restore the version number changed in step 5.