Blank emails in El Capitan Mail.app
To fix this issue there are two ways:


Rebuild


To rebuild a Mailbox in Mail, select the mailbox you want to rebuild and click on the Mailbox menu; at the bottom there is the Rebuild option. Repeat this step for each one of your Mailboxes.

It can take few hours to reindex a large mailbox and if it's an IMAP or Exchange mailbox, the rebuild will have to download again everything from the server.


Reindex


It is also often necessary to manually reindex Mail messages after a major OS upgrade. This is also necessary if Mail becomes unresponsive and/or if search is not functioning correctly or the app doesn't run.


Quit Mail if it’s open.
From the terminal run 

mkdir ~/Desktop/backup
mv ~/Library/Mail/V2/MailData/Envelope\ Index*  ~/Desktop/backup`


(replace V2 with V4 for Sierra).
Launch Mail and it will build new Envelope Index files; that can take a long time if there are many messages to reindex and if it's an IMAP or Exchange mailbox, the rebuild will have to download again everything from the server.


If everything seems to be working correctly, you can now delete the backup from from your desktop (rm ~/Desktop/backup).