1. how to clean up the Audio folder? How do I know there are no unused wave files floating around?
2. how to avoid duplicates? Say I load the same wave file in 2 different sonar files where the sonar files share the same Audio folder, will that give me duplicate's?

1. use the clean audio folder thing. It's under one of the drop down menus. That said, I don't trust it and it's a pain in the ass to use. 

2. read below.

You should be using per project folders. You don't want one audio folder for everything. Organization is a lot easier that way. 
Save all your projects to their own folders. Take your previously used audio folder and move it somewhere. Then open all your new per project files to verify that you did things right. Then delete the original audio folder.

Yes, I totally agree about having "Per Project Folders" activated.

Once you've done this, open up each project in turn, then do a "Save As" to a different location. Make sure you've got "Copy Audio With Project" checked.

Once you've done this for all your projects, you can safely delete the contents of the global audio folder.

But don't delete the folder itself - this needs to be present for those times when you start a new project by the "Ctrl + n" shortcut

I won't even worry about deleting it unless your computer is very very old and sports a 20 Gig hard drive. Just another source of back up I say. 

I do use per project folder, but within 1 project I still might encounter duplciates