The acronym
environment internally uses the description
environment, but the classicthesis
package changes the way description
item labels are displayed. The scrbook
class also makes its own changes.
With just scrbook
, the item labels are displayed in bold sans-serif:
\documentclass{scrbook}
\begin{document}
\begin{description}
\item[ABC] A B C
\end{description}
\end{document}

Adding classicthesis
changes the item label to small-caps:
\documentclass{scrbook}
\usepackage{classicthesis}
\begin{document}
\begin{description}
\item[ABC] A B C
\end{description}
\end{document}

The acronym
package additionally sets the item format (within the acronym
environment) to use \aclabelfont
which defaults to using bold:
\documentclass{scrbook}
\usepackage{classicthesis}
\usepackage{acronym}
\begin{document}
\begin{acronym}
\acro{ABC}[ABC]{A B C}
\end{acronym}
\begin{description}
\item[\aclabelfont{ABC}] A B C
\end{description}
\end{document}

Now there's a warning message in the transcript:
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
The problem here is that there's no bold small-caps font available, so the bold small-caps has been replaced with just bold lower case.
You can restore scrbook
's formatting for the description
environment using:
\renewcommand{\descriptionlabel}[1]{\hspace{\labelsep}\descfont #1}
For example:
\documentclass{scrbook}
\usepackage{classicthesis}
\usepackage{acronym}
\renewcommand{\descriptionlabel}[1]{\hspace{\labelsep}\descfont #1}
\begin{document}
\begin{acronym}
\acro{ABC}[ABC]{A B C}
\end{acronym}
\begin{description}
\item[\aclabelfont{ABC}] A B C
\end{description}
\end{document}
This produces:
