After iPad restore (from iCloud) apps still appear as 'waiting'
Here is a quick and short how-to guide. 

They say:


  A final step involves re-downloading all your apps from the App Store,
  a process that the iPhone/iPad handled automatically.


So my guess, your iPad and iTunes are clever enough to handle it by itself. When they notice an App is already installed, they wil leave it alone. If they find an uninstalled app, it will be installed.