Don't assume the third slide.
with option pagex={1,2,4,5,6}
One method is as follows:
\documentclass{beamer}
\usetheme{Madrid}
\usepackage{tikz}
\usepackage[printwatermark]{xwatermark}
\newsavebox{\wmark}
\sbox{\wmark}{
\parbox{1cm}{\tikz[color=pink,opacity=0.4]\node{Draft};\\%
\tikz[color=pink,opacity=0.5]\node{Do not distribute};}}
\newwatermark*[pagex={1,2,4,5,6}, angle=30, scale=3, xpos=-35, ypos=-10]{\usebox\wmark}
\begin{document}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
Except here \color{red}\insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\end{document}
to replace with
\newwatermark*[pagex={1,2,4,5,6}, angle=30, scale=3, xpos=-35, ypos=-10]{\usebox\wmark}
OR
\newwatermark*[pages=1-2, angle=30, scale=3, xpos=-35, ypos=-10]{\usebox\wmark}
\newwatermark*[pages=4-6, angle=30, scale=3, xpos=-35, ypos=-10]{\usebox\wmark}
output:

Edit: suggestion
\documentclass{beamer}
\usetheme{Madrid}
\usepackage{tikz}
\setbeamertemplate{background canvas}{%
\ifnum \insertframenumber=3
\else
\begin{tikzpicture}[remember picture,overlay]
\draw ([shift={(0,4.5)}]current page.south) node[color=pink,opacity=0.5,align=left,rotate=45,scale=2.5] {Draft\\[5mm] Do not distribute};
\end{tikzpicture}
\fi
}
\begin{document}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
Except here \color{red}\insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\begin{frame}
I want a watermark everywhere \insertframenumber
\end{frame}
\end{document}