longtable: avoiding multiple captions

Use \endfirsthead to define the first table heading (including a \caption), and \endhead for all other headings. See section 3 of the longtable documentation for details.

\documentclass{scrbook}
\usepackage{longtable}
\begin{document}
\listoftables

\renewcommand{\arraystretch}{5.0}
\begin{longtable}[htb]{|p{1in}|p{1in}|}
    \caption{my table}\\
    \hline 
    1 & 2 \\
    \endfirsthead
    \hline 
    1 & 2 \\
    \endhead
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
\end{longtable}
\end{document}

define \endfirsthead

\documentclass{scrbook}
\usepackage{longtable}
\begin{document}
\listoftables

\renewcommand{\arraystretch}{5.0}
\begin{longtable}[htb]{|p{1in}|p{1in}|}
\caption{my table}\\\hline 
        1 & 2 \\
\endfirsthead
\hline
        1 & 2 \\
    \endhead
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
    \hline  a & b  \\ \hline c & d \\ \hline e & f \\
\end{longtable}
\end{document}