Tabular disjoint line

As explained here: https://tex.stackexchange.com/a/88939/231952, it is not a good idea to use vertical rules in tables. In any case, to answer your question, these commands will suffice:

\setlength{\aboverulesep}{0pt}
\setlength{\belowrulesep}{0pt}

Table 1. With booktabs and without vertical rules (best choice):

\begin{tabular}{cc} \toprule
    A & 0.002s \\ 
    B & 0.05s \\
    C & \\ \bottomrule
\end{tabular}

Table 2. Without booktabs (i.e. with standard rules):

\begin{tabular}{|c|c|} \hline
    A & 0.002s \\ 
    B & 0.05s \\
    C & \\ \hline
\end{tabular}

Table 3. With vertical rules and booktabs:

\setlength{\aboverulesep}{0pt}
\setlength{\belowrulesep}{0pt}
\begin{tabular}{|c|c|} \toprule
A & 0.002s \\ 
B & 0.05s \\
C & \\ \bottomrule
\end{tabular}

If you actually want to draw vertical rules compatible with the rules of booktabs (\toprule, bottomrule, \midrule, etc.), although this is not at all in the spirit of booktabs, you should use {NiceTabular} of nicematrix.

\documentclass{article}
\usepackage{nicematrix}
\usepackage{booktabs}

\begin{document}

\begin{table}
\centering
   \begin{NiceTabular}{|c|c|} \toprule
    A & 0.002s \\ 
    B & 0.05s \\
    C & \\ \bottomrule
   \end{NiceTabular}
\caption{}
\end{table}

\end{document}

You need several compilations (because nicematrix uses PGF/Tikz nodes).