siunitx: how can I avoid adding decimal zeroes?
I think what you need is the round-mode=off
switch. Here's your MWE, slightly reworked:
\documentclass{scrbook}
\usepackage[round-mode=places, round-integer-to-decimal, round-precision=2,
table-format = 1.2,
table-number-alignment=center,
round-integer-to-decimal,
output-decimal-marker={,}
]{siunitx}
\usepackage{booktabs}
\begin{document}
\begin{table}
\centering
\sisetup{table-format=1.3, round-precision=3, table-comparator=true, round-integer-to-decimal=false}
\begin{tabular}{S[round-mode=places]S[round-mode=off]}
\toprule
{``Places''} & {``Off''}\\
\midrule
5,2 & 5,2 \\
0,246 & 0,246 \\
<0,002 & <0,002 \\
<0,002 & <0,002 \\
0,007 & 0,007 \\
0,42 & 0,42 \\
6,9 & 6,9 \\
390 & 390 \\
\bottomrule
\end{tabular}
\end{table}
\end{document}