This is most likely a viewer issue: Compiling your MWE with pdfLaTeX, this is the link position of the bookmark VAA I get in the resulting PDF file:
% 10 0 obj
<<
/D [18 0 R /XYZ 28.346 272.126 null]
>>
Converting the coordinates 28.346 272.126 given in PostScript points to centimetres yields a position of (1cm, 9.6cm) relative to the lower left corner of the paper, which is exactly 1cm to the right of the upper left corner (as the default beamer papersize is 12.8cm x 9.6cm). This shift is due to the page margins set by the document class.
So the bookmark should take you a little bit more to the right at most, but not lower than expected as you describe.
Anyway, if this really bugs you, you can try replacing the destination of the bookmark with a direct reference to the page anchor, which should take you exactly to the upper left corner. This can be done by patching the internal commands producing the bookmarks:
\documentclass[xcolor=dvipsnames]{beamer}
\usepackage{etoolbox}
\makeatletter
\patchcmd{\beamer@part}{Outline\the\c@part}{page.\the\c@page}{}{}
\patchcmd{\beamer@section}{Outline\the\c@part.\the\c@section}{page.\the\c@page}{}{}
\patchcmd{\beamer@subsection}{Outline\the\c@part.\the\c@section.\the\c@subsection.\the\c@page}{page.\the\c@page}{}{}
\patchcmd{\beamer@subsubsection}{Outline\the\c@part.\the\c@section.\the\c@subsection.\the\c@subsubsection.\the\c@page}{page.\the\c@page}{}{}
\makeatother
\title[]{MWE}
\begin{document}
\section{VAA}
\begin{frame}
\titlepage
\end{frame}
\section{John Doe}
\begin{frame}[t]{Slide 1}
\end{frame}
\begin{frame}[t]{Slide 1}
\end{frame}
\begin{frame}[t]{Slide 1}
\end{frame}
\end{document}
I don't know if it's worth the effort, however - after all, presentations are normally given in full screen mode where bookmarks are often not available. Furthermore, beamer itself offers excellent navigation features like hyperlinked headlines, which are much more elegant in use than most viewer's built-in functions.
Best Answer
I think this is your problem - (Print) Preview on a Mac does not support hyperlinks. See this post. Here's the suggestion, instead of saving a print preview (from within Preview), rename the original Thesis.pdf to Myname_mysurname.pdf and then recompile Thesis.tex.