One way is to shift up the skip prior to the mid-height \tabucline
with a \\[-1pt]
. See below for 2nd approach.
%Dokumentclass
\documentclass[landscape]{letter}
%Packages
\usepackage[landscape]{geometry}
\usepackage[utf8] {inputenc}
\usepackage {multirow}
\usepackage {tabu}
%Formatting
\pagestyle{empty} %Remove numbering
\begin{document}
\begin{tabu}{ |[1pt] l | l l | l | l |[1pt] }
\tabucline[1 pt]{1-5}
\multicolumn{2}{ |[1pt] l }{ } & \multicolumn{3}{ |[1pt] l |[1pt]}{ } \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & \multicolumn{2}{ l |[1pt] }{ } \\ \hline
y & & \multicolumn{1}{ |[1pt] l | }{ } & \multicolumn{2}{ l |[1pt] }{ } \\[-1pt] \tabucline[1 pt]{3-5}
\hline
x & & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \tabucline[1 pt]{1-5}
\end{tabu}
\end{document}

Alternately, if you want the thin line to bisect the thick line, then the approach: \\[-1pt] \tabucline[1 pt]{3-5}\\[-12.5pt]\hline
works.
%Dokumentclass
\documentclass[landscape]{letter}
%Packages
\usepackage[landscape]{geometry}
\usepackage[utf8] {inputenc}
\usepackage {multirow}
\usepackage {tabu}
%Formatting
\pagestyle{empty} %Remove numbering
\begin{document}
\begin{tabu}{ |[1pt] l | l l | l | l |[1pt] }
\tabucline[1 pt]{1-5}
\multicolumn{2}{ |[1pt] l }{ } & \multicolumn{3}{ |[1pt] l |[1pt]}{ } \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & \multicolumn{2}{ l |[1pt] }{ } \\ \hline
y & & \multicolumn{1}{ |[1pt] l | }{ } & \multicolumn{2}{ l |[1pt] }{ } \\[-1pt] \tabucline[1 pt]{3-5}\\[-12.5pt]
\hline
x & & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \hline
& & \multicolumn{1}{ |[1pt] l | }{ } & & \\ \tabucline[1 pt]{1-5}
\end{tabu}
\end{document}

You could use something like the following:
\documentclass{article}
\usepackage{xcolor,colortbl}
\usepackage{enumitem}
\newlist{tabitemize}{itemize}{1}
\setlist[tabitemize]{label=\textbullet,nosep,after=\strut,align=parleft,leftmargin=*,}
\usepackage{calc}
\newcolumntype{P}[1]{>{\raggedright\arraybackslash}p{#1\textwidth-2\tabcolsep-0.6pt}}
\begin{document}
\noindent
\begin{tabular}{|*6{P{0.16}}|}
\hline
\multicolumn{6}{|c|}{\textbf{Work system snapshot}}\\ \hline
\rowcolor{black!25}\multicolumn{3}{|c}{Customers} & \multicolumn{3}{|c|}{Products \& services}\\ \hline
\multicolumn{3}{|P{0.5}}{
\begin{tabitemize}
\item People who have a need for the Smartdevice
\end{tabitemize}} &
\multicolumn{3}{|P{0.5}|}{
\begin{tabitemize}
\item smartdevice in white
\item smartdevice in black
\end{tabitemize}}\\ \hline
\rowcolor{black!25}\multicolumn{6}{|c|}{Major activities or processes}\\ \hline
\multicolumn{3}{|P{0.5}}{
\begin{tabitemize}
\item Procurement
\item inventory management
\item Sales
\end{tabitemize}} &
\multicolumn{3}{P{0.5}|}{
\begin{tabitemize}
\item Manufactoring
\item Billing System
\end{tabitemize}}\\ \hline
\rowcolor{black!25}\multicolumn{2}{|c|}{Participants} & \multicolumn{2}{c|}{Information} & \multicolumn{2}{c|}{Technologies}\\ \hline
\multicolumn{2}{|P{0.33}|}{
\begin{tabitemize}
\item Owner
\item Employees
\item Customers
\item Users
\end{tabitemize}} &
\multicolumn{2}{P{0.33}|}{
\begin{tabitemize}
\item BOM
\item Order database which consist of: sales-, purchase and production orders)
\item Inventory information
\end{tabitemize}} &
\multicolumn{2}{P{0.33}|}{
\begin{tabitemize}
\item ERP system
\item ME \& MII system
\item Web interface
\end{tabitemize}}\\ \hline
\end{tabular}
\end{document}

To decresae vertical spaces above and below the items, you can add something like ,after=\vspace{-\baselineskip},before=\vspace{-0.5\baselineskip}
to the \setlist
command.
Here are some additional alternative approaches, as you don't really need all the vertical lines to make your table understandable:
\documentclass{article}
\usepackage{booktabs}
\usepackage{enumitem}
\newlist{tabitemize}{itemize}{1}
\setlist[tabitemize]{label=\textbullet,nosep,after=\strut,align=parleft,leftmargin=*,after=\vspace{-\baselineskip},before=\vspace{-0.75\baselineskip}}
\usepackage{calc}
\usepackage{array}
\newcolumntype{P}[1]{>{\raggedright\arraybackslash}p{#1\textwidth-2\tabcolsep}}
\begin{document}
\noindent
\begin{tabular}{*6{P{0.16}}}
\toprule
\multicolumn{6}{c}{\textbf{Work system snapshot}}\\
\midrule
\multicolumn{3}{l}{Customers} & \multicolumn{3}{l}{Products \& services}\\
\midrule
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item People who have a need for the Smartdevice
\end{tabitemize}} &
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item smartdevice in white
\item smartdevice in black
\end{tabitemize}}\\
\midrule
\multicolumn{6}{c}{Major activities or processes}\\
\midrule
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item Procurement
\item inventory management
\item Sales
\end{tabitemize}} &
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item Manufactoring
\item Billing System
\end{tabitemize}}\\
\midrule
\multicolumn{2}{l}{Participants} & \multicolumn{2}{l}{Information} & \multicolumn{2}{l}{Technologies}\\
\midrule
\multicolumn{2}{P{0.33}}{
\begin{tabitemize}
\item Owner
\item Employees
\item Customers
\item Users
\end{tabitemize}} &
\multicolumn{2}{P{0.33}}{
\begin{tabitemize}
\item BOM
\item Order database which consist of: sales-, purchase and production orders)
\item Inventory information
\end{tabitemize}} &
\multicolumn{2}{P{0.33}}{
\begin{tabitemize}
\item ERP system
\item ME \& MII system
\item Web interface
\end{tabitemize}}\\
\bottomrule
\end{tabular}
\end{document}

\documentclass{article}
\usepackage{booktabs}
\usepackage{xcolor,colortbl}
\usepackage{enumitem}
\newlist{tabitemize}{itemize}{1}
\setlist[tabitemize]{label=\textbullet,nosep,after=\strut,align=parleft,leftmargin=*,after=\vspace{-\baselineskip},before=\vspace{-0.5\baselineskip}}
\usepackage{calc}
\newcolumntype{P}[1]{>{\raggedright\arraybackslash}p{#1\textwidth-2\tabcolsep}}
\begin{document}
\noindent
\begin{tabular}{*6{P{0.16}}}
\toprule
\multicolumn{6}{c}{\textbf{Work system snapshot}}\\
\rowcolor{black!25}\multicolumn{3}{l}{Customers} & \multicolumn{3}{l}{Products \& services}\\
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item People who have a need for the Smartdevice
\end{tabitemize}} &
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item smartdevice in white
\item smartdevice in black
\end{tabitemize}}\\
\rowcolor{black!25}\multicolumn{6}{c}{Major activities or processes}\\
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item Procurement
\item Inventory management
\item Sales
\end{tabitemize}} &
\multicolumn{3}{P{0.5}}{
\begin{tabitemize}
\item Manufactoring
\item Billing System
\end{tabitemize}}\\
\rowcolor{black!25}\multicolumn{2}{l}{Participants} & \multicolumn{2}{l}{Information} & \multicolumn{2}{l}{Technologies}\\
\multicolumn{2}{P{0.33}}{
\begin{tabitemize}
\item Owner
\item Employees
\item Customers
\item Users
\end{tabitemize}} &
\multicolumn{2}{P{0.33}}{
\begin{tabitemize}
\item BOM
\item Order database which consist of: sales-, purchase and production orders)
\item Inventory information
\end{tabitemize}} &
\multicolumn{2}{P{0.33}}{
\begin{tabitemize}
\item ERP system
\item ME \& MII system
\item Web interface
\end{tabitemize}}\\
\bottomrule
\end{tabular}
\end{document}

Best Answer
Use a default
tabular
environment without packagebooktabs
and add right before and after the environment:and also use column type
c
instead ofl
, If you want more horizontal space between the columns then use\setlength\tabcolsep{<whatever length>}
.