I want to try to retrieve the best match/(row) for each ID based on their top score.

You want to group the records by id, and sort each group by score.

Hashes are great for grouping.

my %rows_by_id;
while (<CBLAT>) {
    chomp;
    my %row;
    @row{qw( score id )} = ( split /\t/ )[ 0, 9 ];
    my $id = $row{id};
    push @{ $rows_by_id{$id} }, \%row;
}

for my $id (keys %rows_by_id) {  # Add "sort" if desired
    my $rows = $rows_by_id{$id};
    @$rows = sort { $b->{score} <=> $a->{score} } @$rows;
    my $best_row = $rows->[0];
    print("Best score for id $id: $best_row->{score}\n");
}
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