for ( @data ) {
  my ($id,$name,$ref) = split /,/;
  # You may wish to add some error checking to make sure the
  # hash key $id does not already exist
  $keyhash{$id} = { NAME => $name,
            REF  => $ref#,
            #MANY => [],
                  }
}

for ( @data2 ) {
  my ($id,$name,$ref) = split /,/;
  # Warn and do nothing if a record is found for which the
  # $id is not already in %keyhash
  unless ( defined( $keyhash{$id} ) ) {
    warn "No such record $id!\n";
    next;
  }
  push @{$keyhash{$id}{MANY}}, [ $name, $ref ];
}

##Although you may want MANY to be a hash - it really depends on how you want to use your data later.
##Finally, to extract the number of records for each ID,

##print header

print "Customer         #of docs\n";

# A little something to get the plurality correct
for ( keys %keyhash ) {
  my $num = @{$keyhash{$_}{MANY}};
  printf "%s appeared %d %s\n",
    $_,
    $num,
    $num > 1 ? "times" : "time";
}