I do not really understand what you need %used for, but I would calculate the maximum distance like this:

for (my $i = 0; $i < 50; $i++) { #loop over array of hashes (each subs
+et will have 50 keys)
    my $max = 0; # assuming distances are positive...
    foreach my $key1 (keys $subsets[$i]) { #5 keys at each level
        foreach my $key2 (keys $subsets[$i]) { #5 keys at each level
            next unless exists $distance{$key1}{$key2};
            my $dist = $distance{$key1}{$key2};
            $max = $dist if $dist > $max;
        }
    }
    # do something with $max...
}
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