Look at it this way:

$VAR1 = {
  '12349' => [
               {
                 'name' => 'RIC',
                 'reference' => '00y77676',

               }
             ],
  'X334' => [
               {
 
                 'name' => 'MES',
                 'reference' => '0089kkjh9',

               }
             ],
};
my $href = $VAR1->{12349}[0];
print $href, "\n";
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What would you want print to do, if handed a hashref? What it does, is it stringifies the reference, and that's what you are seeing.

print "$_ => $VAR1->{12349}[0]{$_}\n" for keys %{$VAR1->{12349}[0]};
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...will probably get you a little closer to what you want. Your structure is three levels deep. You're not penetrating it deeply enough.