Email order items template from WooCommerce, containing a custom snippet to show a custom SKU for each product - only in admin emails. This file goes into wp-content/themes/your-child-theme/woocommerce/emails.

email-order-items.php

<?php
/**
 * Email Order Items
 *
 * This template can be overridden by copying it to yourtheme/woocommerce/emails/email-order-items.php.
 *
 * HOWEVER, on occasion WooCommerce will need to update template files and you
 * (the theme developer) will need to copy the new files to your theme to
 * maintain compatibility. We try to do this as little as possible, but it does
 * happen. When this occurs the version of the template file will be bumped and
 * the readme will list any important changes.
 *
 * @see     https://docs.woocommerce.com/document/template-structure/
 * @package WooCommerce/Templates/Emails
 * @version 3.4.0
 */

defined( 'ABSPATH' ) || exit;

$text_align = is_rtl() ? 'right' : 'left';

foreach ( $items as $item_id => $item ) :
	$product       = $item->get_product();
	$sku           = '';
	$purchase_note = '';
	$image         = '';

	if ( ! apply_filters( 'woocommerce_order_item_visible', true, $item ) ) {
		continue;
	}

	if ( is_object( $product ) ) {
		$sku           = $product->get_sku();
		$purchase_note = $product->get_purchase_note();
		$image         = $product->get_image( $image_size );
	}

	?>
	<tr class="<?php echo esc_attr( apply_filters( 'woocommerce_order_item_class', 'order_item', $item, $order ) ); ?>">
		<td class="td" style="text-align:<?php echo esc_attr( $text_align ); ?>; vertical-align: middle; font-family: 'Helvetica Neue', Helvetica, Roboto, Arial, sans-serif; word-wrap:break-word;">
		<?php

		// Show title/image etc.
		if ( $show_image ) {
			echo wp_kses_post( apply_filters( 'woocommerce_order_item_thumbnail', $image, $item ) );
		}

		// Product name.
		echo wp_kses_post( apply_filters( 'woocommerce_order_item_name', $item->get_name(), $item, false ) );

		// SKU.
		if ( $show_sku && $sku ) {
			echo wp_kses_post( ' (#' . $sku . ')' );
			// load the custom SKU
			$custom_sku = get_post_meta( $product->get_id(), 'jk_sku', true );
			if ( is_string( $custom_sku ) ) { // only show the custom SKU if it's set
				echo "<br>" . wp_kses_post( "Custom SKU: $custom_sku" ); // change this line if needed
			}
		}

		// allow other plugins to add additional product information here.
		do_action( 'woocommerce_order_item_meta_start', $item_id, $item, $order, $plain_text );

		wc_display_item_meta( $item );

		// allow other plugins to add additional product information here.
		do_action( 'woocommerce_order_item_meta_end', $item_id, $item, $order, $plain_text );

		?>
		</td>
		<td class="td" style="text-align:<?php echo esc_attr( $text_align ); ?>; vertical-align:middle; font-family: 'Helvetica Neue', Helvetica, Roboto, Arial, sans-serif;">
			<?php echo wp_kses_post( apply_filters( 'woocommerce_email_order_item_quantity', $item->get_quantity(), $item ) ); ?>
		</td>
		<td class="td" style="text-align:<?php echo esc_attr( $text_align ); ?>; vertical-align:middle; font-family: 'Helvetica Neue', Helvetica, Roboto, Arial, sans-serif;">
			<?php echo wp_kses_post( $order->get_formatted_line_subtotal( $item ) ); ?>
		</td>
	</tr>
	<?php

	if ( $show_purchase_note && $purchase_note ) {
		?>
		<tr>
			<td colspan="3" style="text-align:<?php echo esc_attr( $text_align ); ?>; vertical-align:middle; font-family: 'Helvetica Neue', Helvetica, Roboto, Arial, sans-serif;">
				<?php
				echo wp_kses_post( wpautop( do_shortcode( $purchase_note ) ) );
				?>
			</td>
		</tr>
		<?php
	}
	?>

<?php endforeach; ?>

Hi, thank you for this! I'm trying to display the custom field text on the single product page instead of the email (through functions.php), but the code doesn't work there. It says, "Call to a member function get_id() on null" Could you possibly tell me how to adapt it? I would really appreciate it. :)

Hi
I found an other solution with the plugin HTML Mail (https://codemiq.com/en/plugins/wp-html-mail-woocommerce/).