How to put numbers in parenthesis in the S column using siunitx package

Instead of providing the option table-parse-only to the siunitx package, you could also provide the -- in my opinion less intrusive -- option input-symbols = (). Doing so tells siunitx to treat the symbols ( and ) as ordinary inputs, i.e., not to assign any special meaning to them (such as denoting uncertainty...).

Two nice features of this approach are (i) you needn't do anything special in the header information of the tabular environment in order to enter the parentheses in the body of the table and (ii) the ability of the siunitx package to align numbers on their decimal points (and to perform any other parsing tasks) is not affected.

\documentclass{article}
\usepackage{booktabs,siunitx}
\sisetup{input-symbols = ()} % "(" and ")" are ordinary inputs
\begin{document}
\begin{table}[ht!]
\caption{caption here} \label{tab:tab1}
\centering
\begin{tabular}{@{}lSSSS@{}}
\toprule
& \multicolumn{4}{c}{Title here} \\
\cmidrule{2-5}
& \multicolumn{2}{c}{[AA]} & \multicolumn{2}{c@{}}{[BB]} \\
\midrule
$var_{12}$ & 1.37 & (4.36) & 1.50 &  (8.91)\\
$var_{13}$ & 1.73 & (8.43) & 1.84 & (10.88)\\
\bottomrule
\end{tabular}
\end{table}
\end{document}

There are two things we should be careful about.

1. parenthesis are used to indicate the uncertainty through the table-figures-uncertainty macro
2. We can use table-parse-only to get the parsing only feature.

For item 1 above, we can hide ( and ) from siunitx by using braces → {(} and {)} so that they are not meant to indicate the uncertainty. table-parse-only gives correct spacing.

Code:

\documentclass{article}
\usepackage{booktabs}
\usepackage{ctable}
\usepackage{siunitx}
\usepackage{multirow}
%\sisetup{detect-weight=true,table-space-text-pre={(},table-space-text-post={)}}

\begin{document}
\ctable[
     caption = {caption here},
     label = {tab:tab1},
     pos = {!ht},
     center
] {@{}lS@{\enskip}>{{(}}S[table-parse-only]<{{)}}S@{\enskip}>{{(}}S[table-parse-only]<{{)}}}{
    \tnote[$\dagger$]{footnote here}
}{ \FL
\multirow{2}{*}{var} & \multicolumn{4}{c}{Title here} \\
\cmidrule{2-5}
    & \multicolumn{2}{c}{[AA]} & \multicolumn{2}{c}{[BB]} \ML
$var_{12}$ & 1.37 & 4.36 & 1.50 & 8.91  \\
$var_{13}$ & 1.73 & 8.43 & 1.84 & 10.88
\LL}
\end{document}