Bold, horizontally and vertically aligned, multiline table headers

Vertical centring of headings is most easily done with tabular and I removed center as it doesn't centre longtables. I reduced the inter column spacing by a bit as your table was slightly too wide for the page.

\documentclass{report}

\usepackage{booktabs}
\usepackage{longtable}
\newcommand*{\thead}[1]{%
\multicolumn{1}{c}{\bfseries\begin{tabular}{@{}c@{}}#1\end{tabular}}}

\begin{document}

\setlength\tabcolsep{5pt}
\begin{longtable}{@{}rcrrcc@{}}
    \toprule
 \thead{ID} &
 \thead{Database name} &
 \thead{Size\\(MB)} & 
\thead{No. of\\records} &
 \thead{Time stamp\\1st record} &
 \thead{Time stamp\\last record} \\
    \midrule
    %\input{tab-metadata} Really long table
    1 & dummie & 2.1 & 33 & dummie & dummie \\
    2 & dummie & 4.3 & 67 & dummie & dummie \\
    \bottomrule
\end{longtable}


\end{document}

Another solution with the makecell package, which is designed precisely to choose both vertical and horizontal alignment and a common formatting in cells with the \thead and \makecell commands. I also loaded cellspace to have a less tight vertical spacing in tables:

\documentclass{report}

\usepackage{booktabs}
\usepackage{longtable}
\usepackage{makecell}
\renewcommand\theadfont{\bfseries}

\usepackage{cellspace}
\setlength\cellspacetoplimit{4pt}
\setlength\cellspacebottomlimit{4pt}

\begin{document}

\begin{center}
  \begin{longtable}{Srcrrcc}
    \toprule
    \thead{ID} & \thead{Database name} & \thead{\shortstack{Size & & & \\(MB)}} & \thead{\shortstack{No. of\\records}} & \thead{\shortstack{Time stamp\\1st record}} & \thead{\shortstack{Time stamp\\last record}} \\
    \midrule
    %\input{tab-metadata} Really long table
    1 & dummie & 2.1 & 33 & dummie & dummie \\
    2 & dummie & 4.3 & 67 & dummie & dummie \\
    \bottomrule
  \end{longtable}
\end{center}

\end{document}