I had a newly launched client site suddenly fail with the white screen of death a few days ago, neither the site of the Admin backend were accessible but just showed the WSOD. After trouble shooting using all the usual methods such as renaming the plugins folder and showing PHP errors etc I then discovered that the 'wp-includes' folder and also the 'themes' folder itself(!) had disappeared from the site. The file permissions seemed to have been changed as well as previously I was unable to edit the .htaccess file as my FTP user didn't have permissions, but at the time of fixing I could ftp and overwrite the .htaccess files and also all the core WordPress files.
After replacing all of the core WordPress files and reuploading the theme the site started to work again, but I noticed that the latest 3.8.2 had been applied. I don't have a real understanding of how the auto-update process works but checking the FTP logs nobody had logged in since the time of launch and then trying to fix it so I'm ruling out somebody accidentally deleting some files via FTP.
So this leads me to be suspicious that the auto-update function deleted these files. So my question as indicated in the title is whether WordPress's auto-update could delete core WordPress files and cause a white screen of death?