If you delete Aux Tracks through their own right click menu, they disappear, yet remain in the list as optional sends, available to all other existing tracks. Shouldn't they disappear from the bus menu?

Yes. They remain active in the project until you Save and Close the project. Once you reopen the project they'll be totally removed. At least that's what the literature is saying. I still haven't install JP yet so I hav enot tested.
 
This is supposedy necessary to make Undo/Redo actions possible. Check out the last eZine for more details on it.
 
Cheers.

Technically, it's not the Aux track that continues to live.  It's the patch point that was associated with the Aux track.  Unless you've renamed the point, it will disappear once it no longer has connections.  If it's been renamed, it will go away when the project is closed and reopened.
 
 

The underlying patch point is kept around for undo and redo. Once you save and reload your project it will be removed if no other track or bus is referencing it.

That all makes good sense. Thanks!