Wouldn't this fail if the same element appears mulitple times in an array, such that the number of times it appears overall is == num of arrays? This code assumes all elements are unique in each array.

The provided code does not make that assumption. The key lines are:

foreach my $k (keys %ids) {
    my %uniq = map { $_ => 1 } @{ $ids{$k} };
    $count[$_]++ for keys %uniq;
}
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If the array in $ids{$k} has a whole bunch of 1s in it, that's okay, we'll overwrite $uniq{1} a whole bunch of times. Because hash keys must be unique.

This means that at the last statement in this loop %uniq will represent a hash with only the unique values from $ids{$k}

I hope this helps.

jarich