A hash is inappropriate here. Your key is not a key at all. A key is a *unique* way of *identifying* something. A score is neither unique, nor an identity.

my @data = (
   [ 12, 'First line of text'  ],
   [ 25, 'Second line of text' ],
   [ 34, 'Third line of text'  ],
);

foreach (@scoreWords) {
   my $re = qr/\b\Q$_\E\b/i;
   foreach (@data) {
      $_[0] += $y while $_[1] =~ /$re/g;
   }
}
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Update: I either missed the second part of the question, or the OP has been updated. Here's my updated answer:

my @data = (
   [ 1, 12, 'First line of text'  ],
   [ 2, 25, 'Second line of text' ],
   [ 3, 34, 'Third line of text'  ],
);

foreach (@scoreWords) {
   my $re = qr/\b\Q$_\E\b/i;
   foreach (@data) {
      $_[1] += $y while $_[2] =~ /$re/g;
   }
}

print("Line ${$_}[0] has a score of ${$_}[1]\n")
   foreach sort { $b->[1] <=> $a->[1] } @data;
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or if you don't actually care about the line numbers:

my @data = (
   [ 12, 'First line of text'  ],
   [ 25, 'Second line of text' ],
   [ 34, 'Third line of text'  ],
);

foreach (@scoreWords) {
   my $re = qr/\b\Q$_\E\b/i;
   foreach (@data) {
      $_[0] += $y while $_[1] =~ /$re/g;
   }
}

print("${$_}[0]: ${$_}[1]\n")
   foreach sort { $b->[0] <=> $a->[0] } @data;
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Update: Changed if // to while //g.