I'd build a temporary hash before array3:

%hash3 = map {
 $_->{year}.$->{month}.$_->{day}.$_->{hhmm}= $_
} @array1;

for(@array2){
 $k=$_->{year}.$->{month}.$_->{day}.$_->{hhmm};
 if(!defined $tmp{$k}){
  $hash3{$k}=$_;
 }else{
  $hash3{$k}->{data2}=$_->{data2};
 }
}
@array3=map { $hash3{$_} } sort keys %hash3;
#or just 
@array3=values %hash3; 
#if you don't care about sorting
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That should be pretty fast if you use map on the larger array (I assumed it is @array1). HTH!
(beware, the code is untested)
Update:

 if(!defined $tmp{$k}){
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should be

 if(!defined $hash3{$k}){
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Well, I'm learning by trial and error, it seems.