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}