Cut bottom of tabular by Zig-Zag pattern (in latex beamer)

The extra padding you are getting is due to the value for node sep for the node containg the tabular; to get the desired result, you can simply set this to 0pt:

\documentclass{beamer}
\usepackage{tikz}
\usetikzlibrary{decorations.pathmorphing}

\begin{document}

\begin{frame}
\centering
\begin{tikzpicture}[ampersand replacement=\&] 
\node[inner sep=0pt] (elenore)
{%
\begin{tabular}{| c | c c | l |} 
\cline{2-3}
\multicolumn{1}{c}{} & \multicolumn{2}{|c|}{Header} \\
\hline
A & B & C & D \\
E & F & G & H \\
I & J & K & L
\end{tabular}%
};
\draw[decoration={zigzag, mirror,segment length=6mm,amplitude=1.1pt}, decorate] 
  (elenore.south west) -- (elenore.south east);
 \end{tikzpicture} 
\end{frame}

\end{document}

Another option would be to draw everything (including the matrix itself) using TikZ:

\documentclass{beamer}
\usepackage{tikz}
\usetikzlibrary{calc,matrix,decorations.pathmorphing}

\tikzset{ 
table/.style={
  matrix of nodes,
  row sep=-\pgflinewidth,
  column sep=-\pgflinewidth,
  nodes={rectangle,text width=3em,align=center},
  text depth=0.25ex,
  text height=1.5ex,
  nodes in empty cells
}
}

\begin{document}

\begin{frame}
\centering
\begin{tikzpicture}[ampersand replacement=\&] 
\matrix (elenore) [table] 
{ 
\& \& \& \\
A \& B \& C \& D \\
E \& F \& G \& H \\
I \& J \& K \& L \\
};
\node at ( $ (elenore-1-2)!0.5!(elenore-1-3) $ ) {Header};
\draw
  (elenore-1-2.south west) |- (elenore-1-3.north east) -- (elenore-1-3.south east);
\draw 
  (elenore-4-1.south west) |- (elenore-2-4.north east) -- (elenore-4-4.south east);
\draw[decoration={zigzag, mirror,segment length=6.25mm}, decorate] 
  (elenore-4-1.south west) -- (elenore-4-4.south east);
 \end{tikzpicture} 
\end{frame}

\end{document}

Just for the fun of it, here's another possibility using the pencildraw style designed by Ipsen in his answer to Torn page effect:

\documentclass{beamer}
\usepackage{tikz}
\usetikzlibrary{calc,matrix,decorations.pathmorphing}

\tikzset{ 
table/.style={
  matrix of nodes,
  row sep=-\pgflinewidth,
  column sep=-\pgflinewidth,
  nodes={rectangle,text width=3em,align=center},
  text depth=0.25ex,
  text height=1.5ex,
  nodes in empty cells,
  column 4/.style={nodes={align=left}}
  },
pencildraw/.style={
    decorate,
    decoration={random steps,segment length=3pt,amplitude=1.5pt}
  }
}

\begin{document}

\begin{frame}
\centering
\begin{tikzpicture}[ampersand replacement=\&] 
\matrix (elenore) [table] 
{ 
\& \& \& \\
A \& B \& C \& D \\
E \& F \& G \& H \\
I \& J \& K \& L \\
};
\node at ( $ (elenore-1-2)!0.5!(elenore-1-3) $ ) {Header};
\draw
  (elenore-4-2.south west) |- (elenore-1-3.north east) -- (elenore-4-3.south east);
\draw 
  (elenore-4-1.south west) |- (elenore-2-4.north east) -- (elenore-4-4.south east);
\draw[pencildraw] 
  (elenore-4-1.south west) -- (elenore-4-4.south east);
 \end{tikzpicture} 
\end{frame}

\end{document}

Using

column <number>/.style={nodes={<options>}}

you can change the attributes for nodes in a column; for example, in the code above I used

 column 4/.style={nodes={align=left}}

to have text aligned left in the fourth column.

You don't have to use tikz

Your tabular example markup generated a lot of errors so I had to make a few guesses as to the intended cells, but something like

\documentclass{beamer}

\begin{document}

\begin{frame}

\sbox0{\begin{tabular}[b]{c| c c | l }
\cline{2-3}
 & \multicolumn{2}{c|}{comparison} &  \\
 \cline{1-4}
 \multicolumn{1}{|c|}{A} & B & C & \multicolumn{1}{l|} {value} \\
 \cline{1-4}
  \multicolumn{1}{|c|}{(1,\texttt{X},\texttt{\$},U,11)} & &   (\texttt{a},\texttt{\$},1) & \multicolumn{1}{l|}{C} \\
  \multicolumn{1}{|c|}{(2,\texttt{r},1,10)} & (\texttt{O},1) & & 
  \multicolumn{1}{l|}{$H_{1} = [\texttt{aa}]$} \\
  \multicolumn{1}{|c|}{(3,\texttt{a},\texttt{a},3,2)} & & (\texttt{a},\texttt{a},6) & \multicolumn{1}{l|}{$H_5 = [\texttt{yyyyyy}]$} \\    
  \multicolumn{1}{|c|}{(4,\texttt{a},5,1)} & (\texttt{a},5) & &
  \multicolumn{1}{l|}{$H = [\texttt{text}]$}\\
\multicolumn{1}{c}{}
\end{tabular}}%
\usebox0\llap{\resizebox{\wd0}{\height}{\fboxsep0pt\colorbox{white}{\strut${\sim}\!{\sim}\!{\sim}$}}}
\end{frame}
\end{document}