I'm wondering if you couldn't rearrange the split and the =~ statement (I don't know if the input array would allow this) .. so you'd do

  #  Delete (something) from the input stream, separate the
  #  count from the file name.

  s/$in_prefix//;
  my ( $count, $file ) = split;
[download]

instead.

As a matter of coding style I use brackets when calling something like split; Since the delimiter is a slash, I'd also avoid the leaning toothpicks by using ' delimiters. So I would write

  #  Decompose directory/sub-directory/file into campaign,
  #  month and file.

  my ( $campaign, $month, $fname ) = split ( '/', $file );
[download]

Finally, I'd probably add the comment that you mentioned already at the top.

#  Build an array of hash references from the output from
#  the output wc -l command containing campaign, month and
#  count data.

my @files = map {
[download]

However, this looks like a situation where a hash of hashes might be more useful -- especially if you want to do subtotals across various months -- or campaigns.

"Excellent. Release the hounds." -- Monty Burns.