Strange. When I use Data::Dumper, I get all the subhashes shown too. Example:

#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;

my %hash= ( 4, {3,4,5,6,7,8});

$hash{a}{b}{c}{d}{e}=366;
print Dumper(\%hash);

#output:

$VAR1 = {
          '4' => {
                   '3' => 4,
                   '7' => 8,
                   '5' => 6
                 },
          'a' => {
                   'b' => {
                            'c' => {
                                     'd' => {
                                              'e' => 366
                                            }
                                   }
                          }
                 }
        };
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Maybe $Data::Dumper::Maxdepth is set to 1 in your script