Vertical spacing in tables with math

You can insert a strut in each row, instead of acting on \arraystretch:

\rowcolors{1}{}{RoyalBlue!20}             % alternate row coloring
\newlength{\oldtabcolsep}                 % keep track of old \tabcolsep
\setlength{\oldtabcolsep}{\tabcolsep}     % 6.0pt
\setlength{\tabcolsep}{0pt}               % so coloring doesn't run off
                                          % ends of the table
\newcommand{\mystrut}{\vrule height 20pt depth 10pt width 0pt }

 \begin{tabular}
   {>{\mystrut}l<{\hspace{\oldtabcolsep}}
    l<{\hspace{\oldtabcolsep}}
    l
   }
\toprule
\multicolumn{1}{l}{Estimator\hspace*{\oldtabcolsep}} & ME & MAE \\
\specialrule{\lightrulewidth}{0pt}{0pt} % so row-coloring aligns
\(\widehat{JV}_{\text{na\"{\i}ve}}\)          & 4.37e-07 & 4.37e-07 \\
\(\widetilde{JV}_{\text{na\"{\i}ve}}\)        & 3.88e-07 & 3.88e-07 \\
\(\widehat{JV}\)                              & 1.33e-06 & 1.33e-06 \\
\(\widetilde{JV}\)                            & 1.20e-06 & 1.20e-06 \\
\bottomrule
\end{tabular}

Since the strut is automatically inserted in the first column, you have to correct it in the header line. Here the dimensions set for the strut are exaggerated; a perhaps satisfying setting may be

\newcommand{\mystrut}{\vrule height 3ex depth 1.5ex width 0pt }

Until now you haven't gave any feedback. Now I will switch my comment to an answer.

First of all don't use the environment center inside the floating environment. An explanation is given in the answer: Should I use center or centering for figures

_{I know inside beamer figure and co. are not floating-environment in the LaTeX meaning.}

---

The package cellspace:

The package cellspace have a simple syntax. It provides only 2 length and a special column prefix S.

The two length are \cellspacebottomlimit and \cellspacetoplimit which can be changed by \setlength. In your example I set both length to 5pt.

\documentclass[xcolor=table,svgnames]{beamer} 
\usepackage{booktabs}
\usepackage{amsmath}
\usepackage{cellspace}
\begin{document}
%==============================================================================%
  \begin{frame}{}
    \begin{table}
    \centering
    \cellspacebottomlimit=5pt
    \cellspacetoplimit=5pt
%      \begin{center}
        \rowcolors{1}{}{RoyalBlue!20}             % alternate row coloring
        \newlength{\oldtabcolsep}                 % keep track of old \tabcolsep
        \setlength{\oldtabcolsep}{\tabcolsep}     % 6.0pt
        \setlength{\tabcolsep}{0pt}               % so coloring doesn't run off
                                                  % ends of the table
        \renewcommand{\arraystretch}{1.3}         % because math expressions
                                                  % almost run into each other
        \begin{tabular}{Sl<{\hspace{\oldtabcolsep}}l<{\hspace{\oldtabcolsep}}l}  
          \toprule
          Estimator & ME & MAE \\
          \specialrule{\lightrulewidth}{0pt}{0pt} % so row-coloring aligns
          \(\widehat{JV}_{\text{na\"{\i}ve}}\)          & 4.37e-07 & 4.37e-07 \\
          \(\widetilde{JV}_{\text{na\"{\i}ve}}\)        & 3.88e-07 & 3.88e-07 \\
          \(\widehat{JV}\)                              & 1.33e-06 & 1.33e-06 \\
          \(\widetilde{JV}\)                            & 1.20e-06 & 1.20e-06 \\
          \bottomrule
        \end{tabular}
%      \end{center}
    \end{table}
  \end{frame}
 \end{document}

The result is seen in picture below:

Note: The package cellspace is incompatible with siunitx. If you want to use both packages you have to create your own file Mycellspace.sty and copy the contents of cellspace in the new file. Now you have to change

\newcolumntype{S}[1]{>{\bcolumn #1\@nil}#1<{\ecolumn}}

to

\newcolumntype{O}[1]{>{\bcolumn #1\@nil}#1<{\ecolumn}}

You need a unknown column type.

---

The package tabu:

The package tabu offers more flexibility as shown below. The package provides the lengths \tabulinesep and \extrarowsep to control the space. In the example I set \tabulinesep=1.5mm

\documentclass[xcolor=table,svgnames]{beamer} 
\usepackage{booktabs}
\usepackage{amsmath}
\usepackage{tabu}

\begin{document}
%==============================================================================%
  \begin{frame}{}
    \begin{table}
    \centering
    \tabulinesep=1.5mm
        \rowcolors{1}{}{RoyalBlue!20}             % alternate row coloring
        \newlength{\oldtabcolsep}                 % keep track of old \tabcolsep
        \setlength{\oldtabcolsep}{\tabcolsep}     % 6.0pt
        \setlength{\tabcolsep}{0pt}               % so coloring doesn't run off
                                                  % ends of the table
        \renewcommand{\arraystretch}{1.3}         % because math expressions
                                                  % almost run into each other
        \begin{tabu}{l<{\hspace{\oldtabcolsep}}l<{\hspace{\oldtabcolsep}}l}  
          \toprule
          Estimator & ME & MAE \\
          \specialrule{\lightrulewidth}{0pt}{0pt} % so row-coloring aligns
          \(\widehat{JV}_{\text{na\"{\i}ve}}\)          & 4.37e-07 & 4.37e-07 \\
          \(\widetilde{JV}_{\text{na\"{\i}ve}}\)        & 3.88e-07 & 3.88e-07 \\
          \(\widehat{JV}\)                              & 1.33e-06 & 1.33e-06 \\
          \(\widetilde{JV}\)                            & 1.20e-06 & 1.20e-06 \\
          \bottomrule
        \end{tabu}
    \end{table}
  \end{frame}
 \end{document}

The result is similar to cellspace but it works with siunitx: