Your specification for the desired result hash is not quite valid: You cannot have a lone array reference in a hash, only  key => value pairs. This can be fixed by giving the array references a key, for example "values". The result hash would then look like this:

( A => { count => 3,
         B => { count => 2, values => ["n1", "n2"] },
         C => { count => 1, values => ["n1"      ] } },
  D => { count => 3,
         E => { count => 2, values => ["n2", "n4"] },
         F => { count => 1, values => ["n1"      ] } } )
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It can easily be generated....

...from the HoH that you already have:

You can transform the existing HoH into the specified result hash, using two (nested) loops, and making use of the fact that  scalar @array gives the number of elements in an array:

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;
}
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...from the original data:

If you do the counting directly in the code that generates the HoH in the first place, it's even easier - just increment the counters for both levels as you go along:

my %hoh;

while (<DATA>) {
    chomp;
    my ($c1, $c2, $c3) = split;
    
    $hoh{$c1}{count}++;
    $hoh{$c1}{$c2}{count}++;
    push @{$hoh{$c1}{$c2}{values}}, $c3;
}

__DATA__
A    B    n1
A    B    n2
A    C    n1
D    E    n2
D    E    n4
D    F    n1
[download]

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Edit: Refactored the answer to make it more structured.