Mail (V4.5) has two search functions - the standard one in the Menu Bar that all applications have (within Help) and another that can be placed in the Tool Bar.
A search using the Tool Bar help will generate mail documents that contain the key word(s) but not the Mailbox. However, the mailbox can be located by clicking on "Show In Mailbox".
The Search function, within Help on the Menu Bar, is quite different. The key word(s) not only locate the Mailbox but also have a floating blue arrow pointing to it.
I wonder why the Mail-specific search function wouldn't also be structured to find Mailboxes, if someone has written the code anyway for the Help search function....unless that's what you mean Lion does.
The Toolbar search is not a Help search, however yes this is where you can search for mailboxes in Lion as well as the usual email contents although it only refines your search instead of revealing it's location.
The reason the Help menu search finds it is because your mailboxes are shown in the menus under Message -> Move to and Message -> Copy to
The floating blue arrow is an standard indicator when you search help for an existing menu item.
So, if you just want to move or a copy an email to the folder, then perhaps the help search would be your best option.
