Update:
In addition to option listof=totoc you can use options bibliography=totoc and index=totoc. Entries for ToC and short ToC can be added to both ToC and short ToC using \setuptoc{toc}{totoc} and \setuptoc{stoc}{totoc}. Then there is also a bookmark for ToC.
Example:
\documentclass[listof=totoc,bibliography=totoc,index=totoc]{scrreprt}
\usepackage[english]{babel}
%\usepackage{caption}% not needed in the example
\addtotoclist[\jobname]{stoc}
\BeforeStartingTOC[stoc]{\value{tocdepth}=0}
\usepackage{xpatch}
\xapptocmd\addtocentrydefault
{\addxcontentsline{stoc}{#1}[#2]{#3}}
{}{\PatchFailed}
\setuptoc{toc}{totoc}% ToC entry in ToC (and short ToC)
\setuptoc{stoc}{totoc}% short ToC entry in ToC (and short ToC)
\usepackage[colorlinks = true,linkcolor = black]{hyperref}
\begin{document}
Here is the Nomenclature...also not covered by second shorter TOC
\listoftoc[Short Contents]{stoc}
\tableofcontents
\listoffigures
\listoftables
\chapter{Introduction}
\section{First Section}
\begin{table}
\caption{Caption of a Table}
\end{table}
\begin{figure}
\caption{Caption of a Figure}
\end{figure}
\section{Second Section}
\end{document}

Example:
Original answer:
If I use option listof=totoc to get a ToC entry for LoF and LoT I can not reproduce the link issue mentioned in the question. To add an entry for ToC in the short ToC use
\AfterTOCHead[toc]{\addxcontentsline{stoc}{chapter}{\contentsname}}
Example:
\documentclass[listof=totoc]{scrreprt}
\usepackage[english]{babel}
%\usepackage{caption}% not needed in the example
\addtotoclist[\jobname]{stoc}
\BeforeStartingTOC[stoc]{\value{tocdepth}=0}
\usepackage{xpatch}
\xapptocmd\addtocentrydefault
{\addxcontentsline{stoc}{#1}[#2]{#3}}
{}{\PatchFailed}
\AfterTOCHead[toc]{\addxcontentsline{stoc}{chapter}{\contentsname}}% ToC entry in short ToC
\usepackage[colorlinks = true,linkcolor = black]{hyperref}
\begin{document}
Here is the Nomenclature...also not covered by second shorter TOC
\listoftoc[Short Contents]{stoc}
\tableofcontents
\listoffigures
\listoftables
\chapter{Introduction}
\section{First Section}
\begin{table}
\caption{Caption of a Table}
\end{table}
\begin{figure}
\caption{Caption of a Figure}
\end{figure}
\section{Second Section}
\end{document}

Note that the patch of \addtocentrydefault only affects ToC entries done by this command or by \addchaptertocentry or \addxcontentsline{toc}{chapter}{...}. If other packages use \addcontentsline directly, you will not get an entry in the short ToC automatically.
Then it could be better to use the scrwfile solution:
\documentclass[listof=totoc]{scrreprt}
\usepackage[english]{babel}
%\usepackage{caption}% not needed in the example
\usepackage{scrwfile}
\TOCclone[Short Contents]{toc}{stoc}
\addtocontents{stoc}{\protect\value{tocdepth}=0}% or \BeforeStartingTOC[stoc]{\value{tocdepth}=0}
\AfterTOCHead[toc]{\addxcontentsline{stoc}{chapter}{\contentsname}}% TOC entry in short TOC
\usepackage[colorlinks = true,linkcolor = black]{hyperref}
\begin{document}
Here is the Nomenclature...also not covered by second shorter TOC
\listoftoc[Short Contents]{stoc}
\tableofcontents
\listoffigures
\listoftables
\chapter{Introduction}
\section{First Section}
\begin{table}
\caption{Caption of a Table}
\end{table}
\begin{figure}
\caption{Caption of a Figure}
\end{figure}
\section{Second Section}
\end{document}
\addxcontensline{toc}{chapter}{chapter title}(note the x in the macro name) or\addchaptertocentry{chapter title}the chapter title would be added to both the normal ToC and the short ToC. But you add the last page of LoF and LoT to the ToCs. You could use class optionlistof=totocto add the entries for LoF and LoT automatically. – esdd May 27 '20 at 22:11