To get the derived statistics, loop over all the indices and count:

my %table;

# The number of items of group $d of length N (where N is 1 to a
# max. length determined elsewhere) found in $b.

for my $file (keys %a) {
   for my $group (keys %{$a{$file}}) {
      for my $subgroup (keys %{$a{$file}{$group}}) {
         for my $length (@{$a{$file}{$group}{$subgroup}}) {
            $table{$file}{$subgroup}[$length]++;
         }
      }
   }
}
[download]

To print out a table, use another nested loop:

my $file = 'xxx';
for my $length (1..$max_length) {
   for my $unique_d (keys %{$a{$file}{$group}}) {
      # printing stuff using $table{$file}{$unique_d}[$length]
   }
}
[download]

Update: fixed a typo in the second comment.