autoref and braces around equation number

If you're not willing -- or allowed! -- to modify some lower-level TeX macros, you could still achieve your objective of getting parentheses placed automatically around cross-referenced equation numbers by (a) executing the following instruction in the preamble:

\usepackage[nameinlink,capitalize]{cleveref}

and (b) using \cref instead of \autoref to generate cross-references.

\documentclass{article}
\usepackage[colorlinks]{hyperref}
\usepackage[nameinlink,capitalize]{cleveref}
\setlength\textwidth{3in} %% just for this example
\begin{document}
\begin{equation}\label{eq:pythag}
a^2+b^2=c^2
\end{equation}
A cross-reference to \cref{eq:pythag} via \verb+\cref+.
\end{document}

For more on various cross-referencing packages and, in particular, the capabilities of hyperref and cleveref in this regard, see the posting Cross-reference packages: which to use, which conflict?

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Addendum: If you must use \autoref and want parentheses placed around the cross-referenced equation numbers, it's necessary to redefine the macro \theequation. Assuming you also use the amsmath package, it's also necessary to modify the auxilliary macro \tagform@. The following MWE shows how this may be done. (The directives \makeatletter and \makeatother are needed because some of the code involves the "special" character @.)

A side remark: If the journal's guidelines prohibit the use of \def in your document, using \renewcommand is probably frowned upon as well. If that's the case, you should probably use \cref instead of \autoref to create cross-references to equations...

\documentclass{article}
\usepackage{amsmath}
\makeatletter
\let\oldtheequation\theequation
\renewcommand\tagform@[1]{\maketag@@@{\ignorespaces#1\unskip\@@italiccorr}}
\renewcommand\theequation{(\oldtheequation)}
\makeatother

\usepackage[colorlinks]{hyperref}
\renewcommand{\equationautorefname}{Eq.}

\usepackage[nameinlink,capitalize]{cleveref}
%% Need to undo the effect of redefinition of "\theequation" to use \cref:
\creflabelformat{equation}{#2\textup{#1}#3}  % No more parentheses around "#1"

\setlength\textwidth{3in} %% just for this example
\begin{document}
\begin{equation}\label{eq:pythag}
a^2+b^2=c^2
\end{equation}

A cross-reference to \autoref{eq:pythag} via \verb+\autoref+.

A cross-reference to Eq.~\eqref{eq:pythag} via \verb+\eqref+.

A cross-reference to \cref{eq:pythag} via \verb+\cref+.
\end{document}

The following example defines \myeqref, which prepends the equation reference by Eq.~ and includes the prefix and the parentheses into the link. The prefix can be overwritten by the first optional argument.

The \autoref name macros do not have access to the counter, thus the following definition of \equationautorefname is just a dirty hack.

\documentclass[a5paper]{article}
\usepackage{amsmath}
\usepackage{hyperref}
\newcommand*{\myeqref}[2][Eq.~]{%
  \hyperref[{#2}]{#1(\ref*{#2})}%
}
\def\equationautorefname#1#2\null{%
  Eq.#1(#2\null)%
}

\begin{document}
\begin{equation}
\label{eq:einstein}
E=mc^2
\end{equation}
References: \myeqref{eq:einstein} and \myeqref[equation~]{eq:einstein}.\\
Reference: \autoref{eq:einstein}.
\end{document}