Here is some sample code to do this:
function hook_form_alter(&$form, &$form_state, $form_id) {
switch($form_id) {
case 'views_exposed_form':
$allowed_categories = db_query("SELECT 1 as tid, "Term Name (2)" as `name`")->fetchAllKeyed();
$allowed_categories = array_reverse($allowed_categories, TRUE);
$allowed_categories['All'] = '- Any -';
$allowed_categories = array_reverse($allowed_categories, TRUE);
$form['field_category_tid']['#options'] = $allowed_categories;
break;
}
}
Just change the query to return 2 columns - the tid and the name with a count.