my %h1 = $csv1->csv_to_hash; # with $csv1 the smallest file

my %temp;
while (my $line = $csv2->next)
{
  my $key = $line->key;
  # Ignore lines that don't also exist in h1
  # That's way less data to build into the second hash
  next unless exists $h1{$key};

  my $value = $line->value;
  $temp{ $key } = [ $h1{$key}, $value ];
}

%h1 = (); # Free the data from %h1, the matching pairs are all in %temp anyway

my %out;
while (my $line = $csv3->next)
{
  my $key = $line->key;
  # As before, ignore non relevant keys
  next unless exists $temp{$key};

  # We make a copy of the array ref from %temp
  # This means that technically modifying it also changes the content of %temp
  # But it will be deleted anyway
  my $values_array = $temp{$key};
  my $value = $line->value;
  
  push @$values_array, $value;
  # Add the values into a brand new hash
  # So that it contains only the needed keys
  $out{$key} = $values_array;
}
%temp = (); # The important keys have been copied to %out;