Redefine the font command \chapterNumber to the font (and scaling factor) you prefer.
\documentclass[12pt,a4paper,openany,twoside=semi,footinclude=true,headinclude=true]{scrbook}
\usepackage[parts,pdfspacing,dottedtoc]{classic thesis}
\font\chapterNumber=pplr9d scaled 6000\relax % Original value: 7000
\begin{document}
\chapter{A title}
\end{document}
Original scaling factor 7000:

Modified scaling factor 6000:

Note that this redefinition will render the package option eulerchapternumbers void. Instead, if you want to use rescaled Euler fonts for the chapter numbers, change the command to
\font\chapterNumber=eurb10 scaled 6000\relax