Apps not loaded on your iPad do not count against your storage limit. Anything in the Purchased tabs of the iStores (Music, Books, TV Shows, Apps) that are not actually on the iPad do not count against your iCloud storage.
On your iPad, they may be adding to your backup sizes. You can explore that under the General > Usage > Manage Storage settings. Turning this off for apps you don't really care to have backed up can save a fair amount of space.
Some apps also use the Documents and Data storage, which you can see in the same place. I don't' recommend deleting stuff directly from Documents and Storage unless you know exactly what you are doing. In most cases it will delete the content from the app as well. Go to the app instead. If you don't want the content on iCloud, the app should have a setting to turn it off.
Mail and it's attachments (in all folders) do count agains't your storage. Check in the same place. To reduce it, go to those folder in Mail (or at icloud.com on a computer) and clean them out.
There are probably a few other things I am forgetting.