Maintaining table format with space between rows

You can use the optional argument of \\ to increase the vertical space between rows and keeping the table format:

\documentclass{book}
\usepackage{booktabs}

\begin{document}

\begin{table}
  \begin{tabular}{l | c c c c | c c c c}
    \multicolumn{1}{c}{} & \multicolumn{4}{c}{Initial Conditions} 
      & \multicolumn{4}{c}{Final Conditions} \\
    Scenario No. & Latitude & Longitude & Altitude & Airspeed & Latitude & Longitude & Altitude 
      & Airspeed \\ \hline
    1-01 & 44.251100 & -75.760474 & 5000 & 75 & 45.095869 & -75.773706 & 1580 & 75 \\
    1-02 & 44.251100 & -75.760474 & 5000 & 75 & 45.998808 & -75.744519 & 1580 & 75 \\[1em]
    1-03 & 44.222150 & -75.395867 & 5000 & 75 & 45.095869 & -75.773706 & 1580 & 75 \\
    1-04 & 44.222150 & -75.395867 & 5000 & 75 & 45.998808 & -75.744519 & 1580 & 75 \\[1em]
    1-05 & 44.084742 & -75.893425 & 5000 & 75 & 45.095869 & -75.773706 & 1580 & 75 \\
    1-06 & 44.084742 & -75.893425 & 5000 & 75 & 45.998808 & -75.744519 & 1580 & 75 \\
\bottomrule
\end{tabular}
\end{table}

\end{document}

The vertical lines are drawn as part of the cell. If you have only \\ and no & you do not create any cells except the very first one, and therefore you won't get vertical lines (or cell background colors).

To fix this you need to add the right number of & for the empty line, so replace \\ with &&&&&&&&\\. If you need this very often you can define it to a macro outside the tabular.