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}
It's not clear that there is really an issue to be solved, it is only an issue for tables if you think there is an issue about tables. Most of the points that you raise could also be made about "paragraphs" or "lists", at some point you have to have some structural information as well as words.
It is easy to have an environment that defaults the column spec, consider for example the amsmath matrix which is more or less just array with a default supplied preamble of *{20}{c} so you could define
\newenvironment{mytab}[1][*{50}{c}]{%
\begin{tabular}{#1}}{%
\end{tabular}}
which makes the column specifications optional, defaulting to all centred. Unlike matrices though where a global default is commonly useful, in my experience a global table default is almost never useful, tables usually have varied column types, some textual, some numeric to be aligned on decimal points, etc. However if in a particular document you have a lot of tables all taking the same form you could use a definition as above, replacing *{50}{c} by say >{\bfseries}l *{2}{D..{3.2}} p{3cm} if all your tables have a bold left aligned column, two numeric columns and a final column of note paragraphs.
It's hard to guess how you could automate rules in general, If you always want a top and bottom rule you could change your definition to
\newenvironment{mytab}[1][*{50}{c}]{%
\begin{tabular}{#1}\toprule}{%
\\\bottomrule\end{tabular}}
But the position of \midrule is rather like the position of words and numbers in the table, effectively it's data that must be entered in each case. Perhaps you only want \midrule after the heading in which case you could use
\newcommand\endhead{\\\midrule}
so your tables would then look like
\begin{mytab}
\hd{type}&\hd{A}&\hd{B}&\hd{Notes}\endhead
zzz&1.2&3.4& zz zz zzzzz\\
zzz&1.2&3.4& zz zz zzzzz\\
\end{tab}
Using a heading command \hd that could be defined as
\newcommand\hd[1]{%
\multicolumn{1}{c}{\bfseries\begin{tabular}{@{}c@{}}#1\end{tabular}}
To give bold, centred, potentially multi-line table headings. Color could be added to this command as well if you want coloured tables, there is no need for explicit colours in the table.
Best Answer
One option is to use the
\extracolsepcommand instead of\hskip, which adds space to the left of the next column rather than at the end of the current one. However, because this affects all subsequent columns, you need to set it back to zero after the next column specifier, and, because this means using@, to avoid suppressing all space there, manually adding back in a space of2\tabcolsep(for the spaces both to the right of that column and the left of the one after that):