Thanks davorg. That does help. For someone else who comes here looking for an answer to this same Q, here is what I did:

$xml = new XML::Simple (KeyAttr=>[],ForceArray=>['substrate','product'
+]);
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So I specifically made all "substrate" and "product" elements into arrays. I then had to figure out the number of elements in that array. And this I did by:

foreach $g (@{$data->{reaction}}){
        $length = scalar @{$g->{substrate}};
        print " $g->{name}, len = $length\n";
}
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Thanks for all your help! Cheers, Bioswami