You can do that by working with the indexes, rather than shifting

my %ns_records = map {
    $ns_list[$_] => [
        $addr_list[$_],
        $ptr_list[$_],
        $uptime_list[$_]
    ]
} 0 .. $#ns_list;
[download]

That is non-destructive of your original data.

A small point of style. The _list suffixes on your arrays don't add much to the readability of your code. I would drop them in favor of descriptive plurals like @addrs, @ptrs, @uptimes. Your hash would read better with a singular name, $ns_record{'foo.org'} pronounced "ns_record of foo.org".

The warning should have a line number associated with it. I think it is from line 33, @{$ns_records{$k}}->[$d], which should be $ns_records{$k}->[$d].