Get only the top level categories. There is no depth parameter on the get_categories function, this query and foreach loop will ensure only toplevel categories are displayed:

<?php
	$args=array(
		'taxonomy' => 'product_cat',
		'hierarchical' => '1',
		'hide_empty' => '0',
		'pad_counts' => '1',
		'orderby' => 'term_order'
	);
	$categories=get_categories($args);
	foreach($categories as $category) { 
		if($category->parent == 0 ){
			echo '<p><a href="'. get_term_link($category->slug, 'product_cat') .'" title="' . sprintf( __( "View all posts in %s" ), $category->name ) . '" ' . '>' . $category->name.'</a> '. $category->count . '</p> ';
		}
	} 
?>

This query will get just the child categories of a given parent:

<?php
	$categoryID =  $category->term_id;
	$args=array(
		'taxonomy' => 'product_cat',
		'child_of' => $categoryID,
		'hide_empty' => '0',
		'orderby' => 'term_order'
	);
	$categories=get_categories($args);
	foreach($categories as $category) { 
		echo '<p>- <a href="'. get_term_link($category->slug, 'product_cat') .'" title="' . sprintf( __( "View all posts in %s" ), $category->name ) . '" ' . '>' . $category->name.'</a> '. $category->count . '</p> ';
	}
?>

In conjunction with the ‘Custom Taxonomy Order‘ plugin and an orderby parameter of ‘term_order’, the two queries above can be combined to return a custom ordered list of categories with multiple levels.

<?php
	$args=array(
		'taxonomy' => 'product_cat',
		'hierarchical' => '1',
		'hide_empty' => '0',
		'pad_counts' => '1',
		'orderby' => 'term_order'
	);
	$categories=get_categories($args);
	foreach($categories as $category) { 
		if($category->parent == 0 ){
			echo '<p><a href="'. get_term_link($category->slug, 'product_cat') .'" title="' . sprintf( __( "View all posts in %s" ), $category->name ) . '" ' . '>' . $category->name.'</a> '. $category->count . '</p> ';
			$categoryID =  $category->term_id;
			$args=array(
				'taxonomy' => 'product_cat',
				'child_of' => $categoryID,
				'hide_empty' => '0',
				'orderby' => 'term_order'
			);
			$categories=get_categories($args);
			foreach($categories as $category) { 
				echo '<p>- <a href="'. get_term_link($category->slug, 'product_cat') .'" title="' . sprintf( __( "View all posts in %s" ), $category->name ) . '" ' . '>' . $category->name.'</a> '. $category->count . '</p> ';
			}
		}
	} 
?>