Have a look at your data structure using Data::Dumper:

use Data::Dumper;
print Dumper $config;

gives you

$VAR1 = {
          'item' => {
                      'AMEX' => {
                                'destination_dir' => 'test',
                                'id' => 0
                              },
                      'bla' => {
                               'destination_dir' => 'test1',
                               'id' => 1
                             },
                      'alb' => {
                               'destination_dir' => 'test2',
                               'id' => 2
                             }
                    }
        };
[download]

So $config->{item} represents a reference to a hash with keys "AMEX", "bla", and "alb". If you try $config->{item}->{1}->{destination_dir}; you are using a key that does not exist, the string "1".

UPDATE: I probably should state explicitely that there is no numeric index in a hash and that there is no defined order of items in a hash that you can rely on.