How can I have a figure or a table in tikzset?

It is possible to reproduce the posted figure illustrating a convolutional neural network without tikzset.

In fact, tikzset won't help here much since each of the seven arrays is different.

I used nicematrix as a tabular environment because it works by creating TikzPGF nodes, so it fits perfectly with tikzpicture, producing a very compact code.

It is the only additional package required. (I commented on the other unused packages for this example)

    % !TeX TS-program = pdflatex

documentclass{article}
%usepackage[utf8]{inputenc}
%usepackage{tabularx}

%usepackage{pifont}
%usepackage{booktabs}
%usepackage{caption}
%usepackage{makecell}
%usepackage{color}
%usepackage{stackengine,amsmath}
%stackMath

usepackage[table]{xcolor}
usepackage{tikz}
usetikzlibrary{shapes.arrows}

%usepackage[boxsize=1.25em, centerboxes]{ytableau}
%usetikzlibrary{tikzmark,arrows.meta}
%newcolumntype{M}{>{centeringmbox{}vfillarraybackslash}m{50pt}<{vfill}}
%deflayersep{2.5cm}

usepackage{nicematrix} % added

begin{document}

newcommand{inputImg}{%
begin{NiceTabular}{*{3}{>{bfseries}c}}[cell-space-top-limit = 6pt,cell-space-bottom-limit = 6pt,
    hvlines, code-before=chessboardcolors{red!15}{gray!15}]    
1   &   -1  &   1     
-1  &   1   &   -1    
1   &   -1  &   1 
CodeAfter
tikz draw[green!80!blue, ultra thick] (row-2-|col-1) -- (row-2-|col-3)-- (row-4-|col-3)-- (row-4-|col-1)-- cycle; 
end{NiceTabular}   
}

newcommand{filteri}{%
    begin{NiceTabular}{*{2}{>{color{green!80!blue}bfseriesfootnotesize}wc{2pt}}}[cell-space-top-limit = 1pt,cell-space-bottom-limit = 1pt,  hvlines, code-before=chessboardcolors{blue!15}{gray!15}]       
    + & -     
    - & +       
end{NiceTabular}
}

newcommand{filterii}{%
    begin{NiceTabular}{*{2}{>{color{green!80!blue}bfseriesfootnotesize}wc{2pt}}}[cell-space-top-limit = 1pt,cell-space-bottom-limit = 1pt,  hvlines, code-before=chessboardcolors{gray!15}{blue!15}]       
    - & +     
    + & -       
end{NiceTabular}
}

newcommand{firstlayeri}{%
begin{NiceTabular}{*{2}{>{bfseries}c}}[cell-space-top-limit = 7pt,cell-space-bottom-limit = 7pt,
    hvlines, code-before=cellcolor{gray!25}{1-1,1-2,2-1}]      
    4                   & -4      
color{green!80!blue}-4 &       
end{NiceTabular}   
}

newcommand{firstlayerii}{%
begin{NiceTabular}{p{9pt} p{9pt}}[cell-space-top-limit = 4pt,cell-space-bottom-limit = 4pt,
    hvlines]        
     &    
     &      
end{NiceTabular}
}

newcommand{resulti}{%
begin{NiceTabular}{p{16pt} p{16pt}}[cell-space-top-limit = 8pt,cell-space-bottom-limit = 8pt,
    hvlines,  code-before=chessboardcolors{white}{gray!25}]        
    &     
    &   
CodeAfter
tikz{%         
    draw[color=red, ultra thick] (row-1-|col-1) -- (row-2-|col-2);  
}           
end{NiceTabular}
}

newcommand{resultii}{%
    begin{NiceTabular}{p{16pt} p{16pt}}[cell-space-top-limit = 8pt,cell-space-bottom-limit = 8pt,
        hvlines]        
        &     
        &           
    end{NiceTabular}
}


begin{tikzpicture}[shorten >=1pt,thick , draw=black!80]
    sffamily
    
    node(x0) at (0,0){inputImg};
    node(x1) at (2,2){filteri}; 
    node (x2) at (2,-2){filterii};
    node (x3) at (4,2){firstlayeri};
    node (x4) at (4,-2){firstlayerii};
    node (x5) at (8,2){resulti};
    node (x6) at (8,-2){resultii};
    
    draw[->] (x0) -- (x3);
    draw[->] (x0) -- (x4);
    draw[->] (x3) -- (x5);
    draw[->] (x4) -- (x6);
end{tikzpicture} 

end{document}

Going back to your code, and using the same technique, I replaced the output rectangle with an array (with its own internal nodes inside!). Only a single line was changed inside of the tikzpicture code.

documentclass{article}
usepackage[utf8]{inputenc}
usepackage{tabularx}
usepackage[table]{xcolor}
usepackage{pifont}
usepackage{booktabs}
usepackage{caption}
usepackage{makecell}
usepackage{color}
usepackage{stackengine,amsmath}
stackMath
usepackage{tikz-cd}
usetikzlibrary{shapes.arrows}
usepackage[boxsize=1.25em, centerboxes]{ytableau}
usetikzlibrary{tikzmark,arrows.meta}
newcolumntype{M}{>{centeringmbox{}vfillarraybackslash}m{50pt}<{vfill}}
deflayersep{2.5cm}

usepackage{nicematrix} % added

begin{document}
    
newcommand{ouputImg}{% added <<<<
begin{NiceTabular}{*{3}{>{sffamily}c}}[cell-space-top-limit = 6pt,cell-space-bottom-limit = 6pt,
    hvlines,code-before=rectanglecolor{red!20}{1-1}{3-3}]  
    32  &   11  &   7     
    9   &   4   &   22    
    15  &   2   &   10 
end{NiceTabular}   
}
    
    begin{tikzpicture}[shorten >=1pt,->,draw=black!50, node distance=layersep]
    tikzstyle{every pin edge}=[<-,shorten <=1pt]
    tikzstyle{neuron}=[rectangle,fill=black!25,minimum size=17pt,inner sep=0pt]
    tikzstyle{input neuron}=[neuron, fill=blue!50];
    tikzstyle{output neuron}=[neuron, fill=red!50];
    tikzstyle{hidden neuron}=[neuron, fill=green!50];
    tikzstyle{annot} = [text width=4em, text centered]

    foreach name / y in {1,...,2}
        node[input neuron, pin=left: y] (I-name) at (0,-y) {};

    foreach name / y in {1,...,3}
        path[yshift=0.5cm]
            node[hidden neuron] (H-name) at (layersep,-y cm) {};

    node[ right of=H-2] (O) {ouputImg};  % <<<<<<<< changed


    foreach source in {1,...,2}
        foreach dest in {1,...,3}
            path (I-source) edge (H-dest);

    foreach source in {1,...,3}
        path (H-source) edge (O);

end{tikzpicture} 

end{document}

See Should tikzset or tikzstyle be used to define TikZ styles?

about using of tikzset or tikzstyle