You get a warning, namely
LaTeX Font Warning: Font shape `OT1/cmss/bx/it' undefined
(Font) using `OT1/cmss/bx/n' instead on input line 7.
which means that sans serif boldface italic is not available with Computer Modern Sans.
You can switch to Latin Modern with \usepackage{lmodern}
or to T1 encoding with \usepackage[T1]{fontenc}
.
You may also want to load textgreek
.
\documentclass{scrbook}
\usepackage[T1]{fontenc}
\usepackage{chemmacros}
\usepackage{textgreek}
\usechemmodule{all}
\chemsetup{greek=textgreek}
\begin{document}
\chapter{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\section{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\subsection{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\subsubsection{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\paragraph{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\subparagraph{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\iupac{\trans-\N,\N'-\a-testo-weirdamide}
\end{document}

For Times, you can adjust textgreek
to use Tempora, but don't use mathptmx
, which is basically a big kludge.
\documentclass{scrbook}
\usepackage[T1]{fontenc}
\usepackage{newtxtext,newtxmath}
\usepackage{chemmacros}
\usepackage{textgreek}
\usechemmodule{all}
\chemsetup{greek=textgreek}
\renewcommand*{\textgreekfontmap}{
{qhv/b/*}{LGR/cmss/bx/*}
{qhv/*/*}{LGR/cmss/*/*}
{*/*/*}{LGR/Tempora-TLF/*/*}}
\begin{document}
\chapter{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\section{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\subsection{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\subsubsection{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\paragraph{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\subparagraph{\iupac{\trans-\N,\N'-\a-testo-weirdamide}}
\iupac{\trans-\N,\N'-\a-testo-weirdamide}
\end{document}

\usepackage[T1]{fontenc}
probably (assuming that you still want them in sans serif).