You might find the task easier if you split it into 2 steps, first create an array with the missing data filled down and then create the hash. For example

#!perl
use strict;
use Spreadsheet::ParseExcel;
use Data::Dumper;

my $filename = "Book2.xls";
my $e = new Spreadsheet::ParseExcel;
my $eBook  = $e->Parse($filename);
my $eSheet = $eBook->{Worksheet}[0];
my ( $row_min, $row_max ) = $eSheet->row_range();
my ( $col_min, $col_max ) = $eSheet->col_range();

# build array filling in blanks
my @row_array =();
my @data_array=();
for my $row ($row_min .. $row_max ){
  for my $col ($col_min .. $col_max){
    my $cell = $eSheet->get_cell( $row, $col );
    if ($cell && $cell->value ne ''){
      $row_array[$col] = $cell->value;
    }
  }
  $data_array[$row] = [@row_array];
}
print Dumper \@data_array;

# convert array to hash
my %data = ();
for my $row ($row_min+1 .. $row_max){
  my %set = ();
  my $master_key = $data_array[$row][$col_min];
  for my $col ($col_min+1 .. $col_max){
    my $key   = $data_array[$row_min][$col];
    $set{$key}= $data_array[$row][$col]
  }
  push @{ $data{$master_key} }, \%set;
}
print Dumper \%data;
[download]

update : push @data_array,[@row_array] changed
to $data_array[$row] = [@row_array] to allow for $row_min not being 0.
poj