foreach my $date (keys %counts){
  my $overallcount = $overallcounts{$date};
  foreach my $word (keys %{$counts{$date}}){
    $counts{$date}{$word."_average"} = sprintf("%.2f", 100 * $counts{$
+date}{$word} / $overallcount);
  }
  $counts{$date}{"_overallcount"} = $overallcount;
}

print Dumper \%counts;
[download]

Which yields:

$VAR1 = {
          '2017-09-30' => {
                            'c' => 1,
                            'b' => 2,
                            'a_average' => '57.14',
                            '_overallcount' => 7,
                            'b_average' => '28.57',
                            'c_average' => '14.29',
                            'a' => 4
                          },
          '2017-09-04' => {
                            'd' => 1,
                            'c_average' => '18.18',
                            '_overallcount' => 11,
                            'b' => 3,
                            'a' => 5,
                            'b_average' => '27.27',
                            'd_average' => '9.09',
                            'c' => 2,
                            'a_average' => '45.45'
                          }
        };
[download]

You can then replace {$word."_average"} with {$word} to overwrite the original values.