How can I make siunitx's num bold?

Not perfectly aligned since bold fonts are wider than non bold. Bold fonts are achieved by siunitx package option detect-weight and use of S column type in third and fourth column:

documentclass[a4paper]{scrartcl}
usepackage[ngerman]{babel}
usepackage[utf8]{inputenc}
usepackage{amssymb,amsmath}
usepackage{booktabs, makecell}
renewcommandtheadfont{normalsize}
usepackage[binary-units,group-separator={,}]{siunitx}
sisetup{per-mode=fraction,
         binary-units=true,
         group-separator = {,},
         range-phrase=-}
DeclareSIUnitpixel{px}
DeclareSIUnitfloat{float}
DeclareSIUnitfloats{floats}

usepackage{etoolbox}% <-- for bold fonts
newcommand{ubold}{fontseries{b}selectfont}% <-- for bold fonts
robustifyubold% <-- for bold fonts

begin{document}

begin{table}[ht]
    centering
    begin{tabular}{cll 
                    S[detect-weight,group-minimum-digits = 4,table-format=5.0]% <-- changed
                    S[detect-weight,group-minimum-digits = 4,table-format=8.0]% <-- changed
                    l}
    toprule
# &    Type                     
        &   thead[tl]{Filters @ Patch size / stride} 
            &   {Parameters}    &   {FLOPs}   & Output size  midrule
   &    Input                    
        &   &           0       &       0   & hphantom{0}1 @ $32times 32$    
1  &    Convolution              
        &   hphantom{0}6 @ $5 times 5 times 1$ / 1 
            &       156         &   307 800 & hphantom{0}textbf{6},@,$mathbf{28times 28}$    
2  &    Scaled average pooling   
        & hphantom{00 @} $2 times 2 hphantom{times 00}$ / 2 
            &        2          &       336 & hphantom{0}6 @ $14times 14$    
3  &    Convolution              
        &   16 @ $5 times 5 times 6$ / 1            
            &   2 416           & ubold 942 400% <-- boldface
                                    & 16 @ $10times 10$ 
4  &    Scaled average pooling   
        &   hphantom{00 @} $2 times 2 hphantom{times 00}$ / 2 
            &        2          &     1 600 & 16 @ hphantom{0}$5times hphantom{0}5$   
5  &    Fully Connected          
        &   120 neurons                      
            & ubold 48 120% <-- boldface
                & 240 000   & 120 
6  &    Fully Connected          
        &   hphantom{0}84 neurons           
                &       10 164  &   20 580  & hphantom{0}84 
7  & Fully Connected (output) 
        &   hphantom{0}10 neurons           
            &               850 &   1 730   & hphantom{0}10  midrule
$sum$  &   &   &        61 710 & 15 144 446& num{9118}
    bottomrule
    end{tabular}
end{table}
end{document}

Note: use of bf is depreciated for + 20 years.

Edit:

Meanwhile (after many years and comments below) many of us learned how to managed boldface digits in S column tables. In original answer was not added option mode=text to sisetup and definition of ubold can also be improved:

...
si    usepackage{etoolbox}% <-- for robustify bold fonts in S columns
    newrobustcmdubold{DeclareFontSeriesDefault[rm]{bf}{b}bfseries}% <-- for bold fonts

    begin{document}
    begin{table}[ht]
        centering
    sisetup{detect-weight,
             mode=text,
             group-minimum-digits = 4}
        begin{tabular}{cll
                        S[table-format=5.0]% <-- changed
                        S[table-format=8.0]% <-- changed
                        l}
setup{per-mode=fraction,
         binary-units=true,
         group-separator = {,},
         range-phrase=-,
         mode=text    % <---  
         }
...

Considerinmg above in MWE gives desired result: