Is this more like what you want? I slightly modified the values for \hsize, used a single tabularx and adapted your page dimensions to geometry(not sure it's exactly what you had in mind, though. Please check):
\documentclass[12pt, a4paper]{report}\usepackage[textwidth=145mm, textheight=247mm, nohead, showframe]{geometry}\let\openright=\clearpage%\usepackage[a-2u]{pdfx}\usepackage[czech]{babel}\usepackage{lmodern}\usepackage[T1]{fontenc}\usepackage{textcomp}\usepackage[utf8]{inputenc}\usepackage{amsmath, graphicx}\usepackage{array}\usepackage{caption}\usepackage[output-decimal-marker={,}]{siunitx}\NewDocumentCommand{\anote}{}{\makebox[0pt][l]{$^*$}}\usepackage[usenames]{xcolor}\usepackage{amsfonts}\usepackage{makecell,threeparttable}\usepackage{amssymb}\usepackage{dcolumn}%\setlength\heavyrulewidth{0.25ex}\usepackage{multirow, tabularx}\newcommand{\mc}[1]{\multicolumn{1}{c}{#1}}\usepackage{ragged2e}\newcolumntype{d}[1]{D{.}{,}{#1}}\newcolumntype{L}{>{\RaggedRight\arraybackslash}X}\newcommand\stack[1]{\multicolumn{1}{c}{\shortstack{#1}}}\newcommand{\angstrom}{\mbox{\normalfont\AA}}\newcolumntype{C}{>{\Centering\arraybackslash\hspace{0pt}}X}\newcommand\mytab[1]{% \bgroup% \setlength\extrarowheight{0pt}% \smash{\begin{tabular}[t]{@{}c@{}} #1 \end{tabular}}% \egroup}%%% code block to handle the OP's follow-up question -- see%%% https://tex.stackexchange.com/a/112002/5001 for the source\usepackage{regexpatch}\makeatletter% Change the `-` delimiter to an active character\xpatchparametertext\@cline{-}{\cA-}{}{}\makeatother\hfuzz=99pt\begin{document}\begin{table}[ht!] \scriptsize \setlength\extrarowheight{2pt} \setlength\tabcolsep{2pt} % default: 6pt \begin{threeparttable} \begin{tabularx}{\textwidth}{|*{5}{C|}>{\hsize=1.5\hsize}C| >{\hsize=0.5\hsize}C| *{3}{C|}} \hline \multirowcell{4}{Veličina} & \multicolumn{3}{c|}{[1]} & \multicolumn{2}{c|}{[2]} & [3] & \multicolumn{3}{c|}{[4]} \\ \cline{2-10} \multicolumn{1}{|c|}{} &\multicolumn{3}{c|}{\multirowcell{1.5}{PHOEBE fotometrie a RV}}& \multirow{3}{=}{\centering POWR analýza} & % \multirow{3}{=}{\centering Řešení světelných křivek a RV} & \multirowcell{3}{CFF }& \multirow{3}{=}{\centering Model malá hmotnost} & \multirow{3}{=}{\centering Model střední hmotnost} & \multirow{3}{=}{\centering Model velká hmotnost} \\[1ex] \cline{2-4}& \multirowcell{1.5}{Řešení I} & \multirowcell{1.5}{Řešení II} &\multirowcell{1.5}{Řešení III} & & & & & &\\ [1.5ex] \hline\noalign{\vskip 0.5ex} \hline $P$ (dny) & & & & & & & & \\ $T_0$ (RJD) & & & & & & & & \\ $e$ ( ) & & & & & & & & \\ $\omega$ (\si{\degree}) & & & & & & & & \\ $K_1$ (\si{\kilo\meter\per\second}) & & & & & & & & \\ $K_2$ (\si{\kilo\meter\per\second}) & & & & & & & & \\ $a$ ($\mathrm{M}_{\odot}$) & & & & & & & & \\ $i$ (\si{\degree}) & & & & & & & \\ $T_1$ (\si{\kelvin}) & & & & & & & \\ $T_2$ (\si{\kelvin}) & & & & & & & \\ $\Omega_1$ (\si{\degree}) & & & & & & & \\ $\Omega_2$ (\si{\degree}) & & & & & & & \\ $q = \dfrac{M_2}{M_1}$ & & & & & & & \\ $M_1$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $M_2$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $R_1$ ($\mathrm{R}_{\odot}$) & & & & & & & \\ $R_2$ ($\mathrm{R}_{\odot}$) & & & & & & & \\ $V_{\gamma}$ (\si{\kilo\meter\per\second}) & & & & & & & \\ \end{tabularx} \begin{tablenotes}[para,flushleft] \item[]\\{[1]} \\ {[2]} \\ {[3]} \\ {[4]} \\ \end{tablenotes}\end{threeparttable} \end{table}\end{document} 
If you don't want vertical lines in the second part of the table, here is a code that realises it:
\begin{table}[ht!] \scriptsize\renewcommand{\cellset}{\renewcommand{\arraystretch}{0.75}\scriptsize} \setlength\extrarowheight{2pt} \setlength\tabcolsep{2pt} % default: 6pt \begin{threeparttable} \begin{tabularx}{\textwidth}{|C|*{3}{C} >{\hsize=0.7\hsize}C >{\hsize=1.3\hsize}Cc*{3}{C}} \hline \multirowcell{4}{Veličina} & \multicolumn{3}{c|}{[1]} & \multicolumn{2}{c|}{[2]} & \multicolumn{1}{c|}{[3]} & \multicolumn{3}{c|}{[4]} \\ \cline{2-10} \multicolumn{1}{|c|}{} &\multicolumn{3}{c|}{\multirowcell{1.5}{PHOEBE fotometrie a RV}}&\multicolumn{1}{c|}{\multirowcell{3}{POWR\\ analýza}} & % \multicolumn{1}{c|}{\multirowcell{3}{Řešení\\ světelných\\ křivek a RV}} & \multicolumn{1}{c|}{ \multirowcell{3}{CFF }}&\multicolumn{1}{c|}{ \multirowcell{3}{Model\\malá\\ hmotnost}} & \multicolumn{1}{c|}{\multirowcell{3}{Model\\ střední\\ hmotnost}} & \multicolumn{1}{c|}{\multirowcell{3}{Model\\ velká\\ hmotnost}} \\[1ex] \cline{2-4}&\multicolumn{1}{c|}{ \multirowcell{1.5}{Řešení I}} & \multicolumn{1}{c|}{\multirowcell{1.5}{Řešení II}} & \multicolumn{1}{c|}{\multirowcell{1.5}{Řešení III}} & \multicolumn{1}{c|}{}& \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} \\ [1.5ex] \hline\noalign{\vskip 0.5ex} \hline $P$ (dny) & & & & & & & & \\ $T₀$ (RJD) & & & & & & & & \\ $e$ ( ) & & & & & & & & \\ $\omega$ (\si{\degree}) & & & & & & & & \\ $K₁$ (\si{\kilo\meter\per\second}) & & & & & & & & \\ $K₂$ (\si{\kilo\meter\per\second}) & & & & & & & & \\ $a$ ($\mathrm{M}_{\odot}$) & & & & & & & & \\ $i$ (\si{\degree}) & & & & & & & \\ $T₁$ (\si{\kelvin}) & & & & & & & \\ $T₂$ (\si{\kelvin}) & & & & & & & \\ $\Omega₁$ (\si{\degree}) & & & & & & & \\ $\Omega₂$ (\si{\degree}) & & & & & & & \\ $q = \dfrac{M₂}{M₁}$ & & & & & & & \\ $M₁$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $M₂$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $R₁$ ($\mathrm{R}_{\odot}$) & & & & & & & \\ $R₂$ ($\mathrm{R}_{\odot}$) & & & & & & & \\ $V_{γ}$ (\si{\kilo\meter\per\second}) & & & & & & & \\ \end{tabularx} \begin{tablenotes}[para,flushleft] \item[]\\{[1]} \\ {[2]} \\ {[3]} \\ {[4]} \\ \end{tablenotes}\end{threeparttable} \end{table}
Edit: Here is a code for your last requirement:
\begin{table}[ht!] \scriptsize \renewcommand{\cellset}{\renewcommand{\arraystretch}{0.75}\scriptsize} \setlength\extrarowheight{2pt} \setlength\tabcolsep{2pt} % default: 6pt \begin{threeparttable} \begin{tabularx}{\textwidth}{C|*{2}{C} >{\hsize=0.7\hsize}C >{\hsize=1.3\hsize}Cc*{3}{C}} \Xhline{0.8pt}\noalign{\vskip 0.4ex}\Xhline{0.8pt}% \multirowcell{4}{Veličina} & \multicolumn{2}{c|}{[1]} & \multicolumn{2}{c|}{[2]} & \multicolumn{1}{c|}{[3]} & \multicolumn{3}{c|}{[4]} \\[0.4ex] \cline{2-9} \multicolumn{1}{|c|}{} &\multicolumn{2}{c|}{\multirowcell{1.5}{PHOEBE fotometrie a RV}}&\multicolumn{1}{c|}{\multirowcell{3}{POWR\\ analýza}} & % \multicolumn{1}{c|}{\multirowcell{3}{Řešení\\ světelných\\ křivek a RV}} & \multicolumn{1}{c|}{ \multirowcell{3}{CFF }}&\multicolumn{1}{c|}{ \multirowcell{3}{Model\\malá\\ hmotnost}} & \multicolumn{1}{c|}{\multirowcell{3}{Model\\ střední\\ hmotnost}} & \multicolumn{1}{c|}{\multirowcell{3}{Model\\ velká\\ hmotnost}} \\[1ex] \cline{2-3}& \multicolumn{1}{c|}{\multirowcell{1.5}{Řešení II}} & \multicolumn{1} `{c|}{\multirowcell{1.5}{Řešení III}} & \multicolumn{1}{c|}{}& \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} & \multicolumn{1}{c|}{} \\ [1.5ex]` \Xhline{0.8pt}% $P$ (dny) & & & & & & & \\ $T_0$ (RJD) & & & & & & && \\ $e$ ( ) & & & & & & & \\ $\omega$ (\si{\degree}) & & & & & & & \\ $K_1$ (\si{\kilo\meter\per\second}) & & & & & & & \\ $K_2$ (\si{\kilo\meter\per\second}) & & & & & & & \\ $a$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $i$ (\si{\degree}) & & & & & & & \\ $T_1$ (\si{\kelvin}) & & & & & & & \\ $T_2$ (\si{\kelvin}) & & & & & & & \\ $\Omega_1$ (\si{\degree}) & & & & & & & \\ $\Omega_2$ (\si{\degree}) & & & & & & & \\ $q = \dfrac{M_2}{M_1}$ & & & & & & & \\ $M_1$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $M_2$ ($\mathrm{M}_{\odot}$) & & & & & & & \\ $R_1$ ($\mathrm{R}_{\odot}$) & & & & & & & \\ $R_2$ ($\mathrm{R}_{\odot}$) & & & & & & & \\ $V_{\gamma }$ (\si{\kilo\meter\per\second}) & & & & & & & \\ \end{tabularx} \begin{tablenotes}[para,flushleft] \item[]\\{[1]} \\ {[2]} \\ {[3]} \\ {[4]} \\ \end{tablenotes} \end{threeparttable} \end{table}