the counter in beamer changed with pause

If you don't mind, I would like to suggest an alternative approach instead if trying to solve your actual question:

Beamer already has mechanism in place to display numbered definitions etc. Normally they are inside beamer blocks, but if you want them to be inline as in your example, you can simply adjust their definition.

\documentclass{beamer}

\usecolortheme{orchid}

\makeatletter
\setbeamertemplate{theorem begin}{%
    \inserttheoremname
    \inserttheoremnumber
    \space
}

\setbeamertemplate{theorem end}{}
\makeatother


\begin{document}
    \begin{frame}{A theorem in a box}
        \begin{definition}
            bla
        \end{definition}

        \begin{definition}
            bla
        \end{definition}

        test hello ~\\ \pause
        hello test \pause

        \begin{itemize}
           \item aa \pause
           \item bb \pause
           \item cc
           \item \begin{definition}
                    bla
                 \end{definition}
        \end{itemize}

        \begin{definition}
            bla
        \end{definition}
    \end{frame} 
\end{document}

The reason for the behavior you get, is that with every \pause you actually create a new page in the resulting PDF. That means, with every \pause the compiler loops again over your entire frame. So after the first run the counter is at 4, processing the next \pause with a new frame it will continue with 5.

The answer from samcarter is the elegant solution, the following is a quick-and-dirty workaround:

You just need to reset the counter at the beginning of the frame to the value it was before creating the first frame:

 \setcounter{preFrameDefNum}{\value{DefNum}}
 \begin{frame}{test}
 \setcounter{DefNum}{\value{preFrameDefNum}}

You can automate the first command by:

\usepackage{etoolbox}
\AtBeginEnvironment{frame}{\setcounter{preFrameDefNum}{\value{DefNum}}}

---

Full MWE

\documentclass[serif,envcountsect]{beamer}

\newcounter{DefNum}
\newcounter{preFrameDefNum}
\usecounter{DefNum}
\newcommand{\defi}{\noindent\text{Definition \arabic{DefNum}}\refstepcounter{DefNum}}
\setcounter{DefNum}{1}

\begin{document}

\setcounter{preFrameDefNum}{\value{DefNum}}
\begin{frame}{test} 
\setcounter{DefNum}{\value{preFrameDefNum}}

\defi

\defi

test hello ~\\ \pause
hello test \pause

\begin{itemize}
  \item aa \pause
  \item bb \pause
  \item cc
  \item \defi
\end{itemize}

\defi
\end{frame}
\end{document}