#! /usr/bin/perl
use strict;
use warnings;

use Data::Dumper;
local $Data::Dumper::Useqq = 1;
use Getopt::Long qw(GetOptions);;

...

open(my $table1,'<', $input) or die "$! - [$input]"; #input file 
open(my $table3, '+>', $output) || die ("Can't write new file: $!"); #output file

...

chomp( my @header_for_table1 = split /\t/, <$table1> );

print $table3 join "\t", @header_for_table1, "name1", "name2", "\n";

{
    no warnings 'uninitialized';
    while(<$table1>){
         chomp;
         my %row;
         @row{@header_for_table1} = split /\t/;
         print $table3 join ( "\t", @row{@header_for_table1},
                   @{ $lookup{ ... }
                        // [ "", "" ] }), "\n";
}
}