Is there an automated documentation tool like Javadoc or Doxygen for AutoIt? Or an AutoIt plugin for Doxygen?
Sortof. AutoIt UDFs use a header format which is converted to chm form using a several stage process which is not really designed for public usage but can be found here.
That is the official one. However, there are a number of user submitted variants on the forum such as this one which may be better suited to your needs.
As far as I am aware there is no plugin for Doxygen, and there is no plans for it either.