The trick is to do a Spotlight search in the Finder, but with the starting point already in the Time Machine.
- Open a Finder window and navigate in the Time Machine all the way in the computer's folder, so that the Finder window displays the list of snapshots.
- Enter the search query in the Finder search box.
- Click the + on the right side to add a search parameter: Kind is Other. A box will appear for entering the value; enter mail here.
- Click the + again to enter another search parameters: System files are included.
The Finder will consult the Spotlight database for the Time Machine, and display all of the matching mail messages, across all of the snapshots.
You can use QuickLook (the spacebar) to view any message.
The path bar at the bottom of the window shows the (long) path leading to the mail message. About halfway down the path, and one of the few folders with an recognizable name, is the .mbox folder that contains the message. The name of this folder corresponds to which Mail folder contains the selected message.