Can't tell for sure... but your problem might just be that @label and @labels are two different variables.  (Had you been using strictures, you'd probably have caught that typo yourself...)

#!/usr/bin/perl

use strict;
use warnings;

my $hostname = "foo.bar";

my @labels;
my $nlabels = 0;

for (split /\./, $hostname) {
    push @labels, length, $_;
    $nlabels++;
}

print "\n@labels\n";

my $question = pack("(C a*)$nlabels C n2", @labels,0,1,1);

print '$question: ', join(" ", unpack("(H2)*", $question) ), "\n";  # 
+hexdump

# -->  $question: 03 66 6f 6f 03 62 61 72 00 00 01 00 01
#                    f  o  o     b  a  r
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