Many differently-named emlx files of the same message
Using Spotlight, I can readily find text from within a Mail message. But I have begun to find that there are many copies of the same message, each with its own filename (in the format 1234567.emlx), each in a different folder. It makes me think that moving a message from Inbox to a folder (which Mail seems misleadingly to call a "Mailbox") creates a new file with a new name for the same message. This seems to wasting a great deal of space, and also causing me a great deal of confusion.
Is really the way it 'sposed to be? Or is the presence of all these duplicate-content files a sign that I have configured things wrongly, ot otherwise loused up?
What's a safe way to get rid of these duplicates?