my %hash3_origin = ( 'key1' => [1, 2], 'key2' => [3, 4], 'key3' => [5, 6] ) ;
my @keys3_0 = qw( key1 key1 key2 key2 key2 ) ;
my @keys3_1 = qw( key2 key3 key3 key3 key3 ) ;
my %hash3 ;
my @keys3_origin = keys %hash3_origin ;

@hash3{@keys3_origin} = ([0, 0]) x @keys3_origin ;

foreach ( @keys3_0 ) {
	my $key = $_ ;
	$hash3{ $key }->[0] += $hash3_origin{ $key }->[0] ;
}
foreach ( @keys3_1 ) {
	my $key = $_ ;
	$hash3{ $key }->[1] += $hash3_origin{ $key }->[1] ;
}
print Dumper( \%hash3 ) ;
__END__
$VAR1 = {
          'key3' => [
                      11,
                      28
                    ],
          'key1' => $VAR1->{'key3'},
          'key2' => $VAR1->{'key3'}
        };