Why does the head line disappear under the logo?

Apparently, the horizontal rule sits just above the baseline, so the picture overlaps it and, being printed later, it makes it invisible.

Raise the picture by the rule height (0.4pt) and you're done.

I also suggest not to use scale, but height. Smashing the picture with the optional arguments [0pt][0pt] to \raisebox makes it easier to accommodate the picture without disrupting the vertical placement of the main part of the header.

\documentclass[
  a4paper,
  foldmarks=true,
  fromrule=afteraddress,
  fromphone,
  fromemail,
  fromlogo,
  version=last,
]{scrlttr2}
%\usepackage[utf8]{inputenc}
\usepackage[ngerman]{babel}
\usepackage{graphicx}

\begin{document}

\setkomavar{fromname}{Diane Mustermann}
\setkomavar{fromaddress}{In der Musterstr. 10\\
                        66666 Musterstadt}

\setkomavar{fromphone}{0\,12\,34~56\,78}
\setkomavar{fromemail}{[email protected]}
\setkomavar{fromlogo}{\raisebox{0.4pt}[0pt][0pt]{\includegraphics[height=75pt]{DP}}}

\begin{letter}{%
    Max Mustermann\\
    Haupt Str. 10\\
    99999 Testhausen%
}

\opening{Sehr geehrte Damen und Herren,}
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. 
Aenean commodo ligula eget dolor. Aenean massa. Cum sociis 
natoque penatibus et magnis dis parturient montes, nascetur 
ridiculus mus. Donec quam felis, ultricies nec, pellentesque 
eu, pretium quis, sem. Nulla consequat massa quis enim. Donec 
pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. 
In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. 
Nullam dictum felis eu pede mollis pretium. Integer tincidunt. 
Cras dapibus. Vivamus elementum semper nisi. Aenean vulputate 
eleifend tellus. Aenean leo ligula, porttitor eu, consequat vitae, 
eleifend ac, enim. Aliquam lorem ante, dapibus in, viverra quis, 
feugiat a, tellus. Phasellus viverra nulla ut metus varius laoreet. 
Quisque rutrum. Aenean imperdiet. Etiam ultricies nisi vel augue. 
\closing{Mit freundlichen Grüßen}
\ps PS: Bitte beachten.
\setkomavar*{enclseparator}{Anlage}
\encl{Auszug aus einem Text um die Seite zu füllen}
\cc{Der Vorstand\\Geschäftsführung}

\end{letter}
\end{document}

Note: in the code I changed the name of the picture, fix it for your setup.