Yes, you can create notes in an agenda that is offline. You make notes in offline mode in the same way as in online mode.
When you are offline, you will be able to see where in the document you have your notes. They are displayed using a blue speech bubble, as in online.
Your highlights can be seen when offline, as well as you can make new highlights in offline mode. As soon as you're online again, your offline highlights will be synced to the latest version of the agenda. This means, that if a newer version of the agenda has been published while offline, your highlights will be synced to the latest version.