How to color a particular hexagon based on its coordination address?

Just overwrite the node, e.g. the 3-4 node can be overwritten with

\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{shapes}

\begin{document}
    \begin{tikzpicture} [hexa/.style= {shape=regular polygon,regular polygon sides=6,minimum size=1cm, draw,inner sep=0,anchor=south,fill=lightgray!85!blue,rotate=30}]
    \foreach \j in {0,...,5}{%
        \pgfmathsetmacro\end{5+\j} 
        \foreach \i in {0,...,\end}{%
            \node[hexa] (h\i;\j) at ({(\i-\j/2)*sin(60)},{\j*0.75}) {};}  }      
    \foreach \j in {0,...,4}{%
        \pgfmathsetmacro\end{9-\j} 
        \foreach \i in {0,...,\end}{%
            \pgfmathtruncatemacro\k{\j+6}  
            \node[hexa] (h\i;\k) at ({(\i+\j/2-2)*sin(60)},{4.5+\j*0.75}) {};}  } 
    \node[hexa,fill=red] at (h3;4.south){}; 
    \end{tikzpicture}
\end{document}   

You can use .try handler to overwrite the style of some particular hexagons.

\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{shapes.geometric}
\begin{document}
  \begin{tikzpicture} [
    hexa/.style= {
      shape=regular polygon,
      regular polygon sides=6,
      minimum size=1cm, inner sep=0,
      rotate=30,
      draw, fill=lightgray!85!blue,
    },
    h2.3/.style={fill=red},   % <-- new style
    h5.4/.style={fill=yellow} % <-- new style
  ]
  \foreach \j in {0,...,5}{%
    \pgfmathsetmacro\end{5+\j}
    \foreach \i in {0,...,\end}{%
      \node[hexa, h\i.\j/.try] (h\i;\j) at ({(\i-\j/2)*sin(60)},{\j*0.75}) {};
    }
  }
  \foreach \j in {0,...,4}{%
    \pgfmathsetmacro\end{9-\j}
    \foreach \i in {0,...,\end}{%
      \pgfmathtruncatemacro\k{\j+6}
      \node[hexa,h\i.\k/.try] (h\i;\k) at ({(\i+\j/2-2)*sin(60)},{4.5+\j*0.75}) {};
    }
  }
  \end{tikzpicture}
\end{document}

And to draw your hexagons, you can use some shorter code taken and adapted from here:

\documentclass[border=7pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{shapes.geometric}
\tikzset{
  hexagone/.style={
    shape=regular polygon,
    regular polygon sides=6,
    minimum size=1cm, inner sep=0,
    rotate=30,
    draw, fill=lightgray!85!blue,
    h#1/.try,
    % label={[red]center:#1} % <- uncoment to see the labels
  },
  h3/.style={fill=yellow},  % <- custom style
  h31/.style={fill=red}     % <- custom style
}
\begin{document}
  \begin{tikzpicture}
    \node[hexagone=0] at (0,0){};
    \foreach \r in {1,...,5}
      \foreach \t in {0,...,5}
        \foreach[evaluate={\l=int(\r*(\r-1)*3+\r*\t+\u)}] \u in {1,...,\r}
          \scoped[rotate=-\t*60+30]
            \node[hexagone=\l] at (0+.75*\u,{0.43301270189*(2*\r-\u)}){};
  \end{tikzpicture}
\end{document}