
答え1
LyXでどうやるのかは分かりませんが、
\setcounter{secnumdepth}{4}
文書の序文に追加すれば十分です。
\documentclass{scrbook}
\usepackage{classicthesis}
\setcounter{secnumdepth}{4}
\begin{document}
\mainmatter
\chapter{A}
\section{B}
\subsection{C}
\subsubsection{D}
Is it numbered?
\end{document}
私が実際に使用したコードはtitlesec 2.10.1で、
\documentclass{scrbook}
\usepackage{classicthesis}
\setcounter{secnumdepth}{4}
%% This is only necessary if you have titlesec
%% version 2.10.1 (released 2016/03/15).
%% Version 2.10.2 should fix the bug, which
%% doesn't affect older versions.
\usepackage{etoolbox}
\makeatletter
\patchcmd{\ttlh@hang}{\parindent\z@}{\parindent\z@\leavevmode}{}{}
\patchcmd{\ttlh@hang}{\noindent}{}{}{}
\makeatother
%% End of workaround
\begin{document}
\mainmatter
\chapter{A}
\section{B}
\subsection{C}
\subsubsection{D}
Is it numbered?
\end{document}