Display a custom message for WooCommerce subscription products in order complete email. Goes in your theme's functions.php or as a plugin. Credits: Patrick Garman (@pmgarman)

gistfile1.php

<?php
/* Custom message for subscription products in order complete email */
add_action( 'woocommerce_email_after_order_table', 'wc_completed_email_snippet' );
function wc_completed_email_snippet( $order ) {
	$order_statuses = array( 'completed' ); // order statuses to enable the email on
	$display_cats = array( 148, 149 ); // cat ID's of products to display the message on completed emails for

	if( in_array( $order->status, $order_statuses ) )
		return; // only completed orders
	if( !class_exists( 'WC_Subscriptions_Order' ) || !class_exists( 'WC_Subscriptions_Renewal_Order' ) )
		return; // make sure subscriptions is installed and active
	if( !WC_Subscriptions_Order::order_contains_subscription( $order ) )
		return; // is this a subscription order?
	if( $order->post_parent > 0 )
		return; // if there is a post parent then this is a renewal

	foreach( $order->get_items() as $item ) 
		foreach( wp_get_post_terms( $item['id'], 'product_cat' ) as $term )
			if( in_array( $term->term_id, $display_cats ) )
				$display = true;

	if( $display )
		echo '<strong>A custom note</strong>';

}