The documents that you saved into iCloud are accessible only from within the app that is used to create them. This is by design. Thus when you look at the list of documents from within Keynote app, you are not able to see documents created by Pages. Each app has a separate document folder in iCloud.
You can however delete iCloud documents from Settings app in iOS or from OS X Preferences. This is useful for example when you no longer have the apps installed on your devices. When you remove an app from all your iOS devices and Macs, the iCloud documents created by the app will not be removed automatically.
On iOS, go to Settings > iCloud > Storage & Backup > Manage Storage. You will see a list of apps that has iCloud documents. You can manage iCloud documents for both iOS and OS X apps. As you can see from screenshot below, there is no equivalent of TextEdit and Pixelmator for iOS, but you can still manage their documents on iOS.
Tap on an app and you’ll see all the iCloud files for the app. Tap on the Edit button to get into edit mode. You can now delete the document individually, or use the Delete All button to remove all files at once.
Please note that file deletion is permanent. Once a file is removed from iCloud, you will not be able to access it from all your iOS devices and Macs.
To manage your iCloud documents on the Mac, go to System Preferences > iCloud and click on the Manage… button located at bottom right corner.
You can see that the iCloud preference pane on OS X offers the same options as iOS Settings for managing your iCloud documents.