Rather than fiddle with the definition of \autoref, you can use the \tagform@ command (provided by the amsmath package) to insert parentheses automatically around cross-referenced equation numbers. This works regardless of the cross-referencing command (\ref, \autoref, etc) you employ. The following MWE shows how this may be done:
\documentclass{article}
\usepackage{amsmath,hyperref}
\hypersetup{colorlinks=true}
% First, save the current form of `\theequation`
\let\oldtheequation\theequation
\makeatletter
\def\tagform@#1{\maketag@@@{\ignorespaces#1\unskip\@@italiccorr}}
\renewcommand{\theequation}{(\oldtheequation)}
\makeatother
\begin{document}
\begin{equation}\label{eq:pythagoras}
a^2+b^2=c^2\,.
\end{equation}
Looking at equation \ref{eq:pythagoras}, equation \eqref{eq:pythagoras}, or
\autoref{eq:pythagoras}, \ldots
\end{document}

"As may be seen by the expressions given in equations 1 and 2, 3 out of 4 dentists recommend Brand-X tooth paste to their patients."To me, not placing parentheses around the first two numerals looks clearly wrong... – Mico Apr 18 '12 at 19:36