Autoexec.bat is a critical system process written in the Batch coding language. It instructs what the computer should do on bootup, and thus it should be in the C:\ directory. Deleting this file would not do anything, except from ceasing to run that code on startup. It was last used as a critical system process in Windows XP, and has since became an optional file.
Exploitations by Viruses
As far as system processes go, this is easily the most exploitable. Viruses are able to write their own code to the Autoexec.bat file, which can do anything from triggering payloads to silently formatting the drive on startup. This may have been one of the reasons it was removed. An example is the Pikachu virus.