my %hoh = ( A => { B => [ "n1", "n2" ],
                   C => [ "n1"       ] },
            D => { E => [ "n2", "n4" ],
                   F => [ "n1"       ] }, );

foreach my $col1 (keys %hoh) {
    my $count1 = 0;
    
    foreach my $col2 (keys %{$hoh{$col1}}) {
        my $count2 = scalar @{$hoh{$col1}{$col2}};
        
        $hoh{$col1}{$col2} = { count => $count2,
                               values => $hoh{$col1}{$col2} };
        
        $count1 += $count2;
    }
    
    $hoh{$col1}{count} = $count1;
}