The idea of using an array and specify indexes I didn't really understand the benefit of at first glance.

The idea is to eliminate as much code as possible specifically from the parts that run for each pattern and each text string. This means this bit:

while (my($text_id,$text) = each(%hash2) ) {
      if ($text =~ $match)
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Which, for each iteration, does this:

• each returns the key and value
• those are copied in a list assigment
• the match is attempted

Both the copy and the overhead of the list assignment (which is not insignificant, when repeated a billion times) aren't necessary.

If the text strings are unique, such that you can determine the $text_id given $text, you can leave out the array stuff and just do this:

   my @text = values %hash2;
   my %reverse_hash2 = reverse %hash2;

   while ( my($pattern,$high_lvl_id) = each(%hash1) ) {
       my $match = qr/\b$pattern\b/;
       for my $text (@text) {
           if ( $text =~ $match ) {
               my $text_id = $reverese_hash2{$text};
               ...
           }
       }
   }
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Because for (@array) doesn't copy array but just iterates over it, and $text is aliased to each element in turn, not copied over it, this should be faster.