First, change @{$ns_records{$k}}->[$d] to $ns_records{$k}->[$d], and your warning goes away. You are trying to use an array as an arrayref, as the warning states. You wouldn't normally say "@array[0]" (that would be a slice). You would say "$array[0]". Dealing with references doesn't change how sigils are applied.

And here's another (and to me, clearer) way to build the datastructure.

use strict;
use warnings;

use Data::Dumper;

    my @ns_list = ( 'server1.foo-domain.net',
                    'server2.noo-domain.net',
                    'server3.zoo-domain.net', );

  my @addr_list = ( '1.2.3.5',
                    '11.22.33.55',
                    '22.21.20.55', );

   my @ptr_list = ( '5.3.2.1.in-addr.arpa',
                    '55.33.22.11.in-addr.arpa',
                    '55.20.21.22.in-addr.arpa', );

my @uptime_list = ( '131 days',
                    '28 days',
                    '366 days', );

my %hash;

$hash{$ns_list[$_]} = [ $addr_list[$_], 
                        $ptr_list[$_], 
                        $uptime_list[$_]
                      ] for 0 .. $#ns_list;
                      
print Dumper \%hash;
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