facetwp index a field in a related post type

custom-hooks.php

<?php
/**
 ** look up and index a value from a post relationship field
 ** set the datasource to the relationship field
 ** get the post id of that related post and use it to
 ** lookup its associated value
 ** for ACF you may want get_field() instead of get_post_meta()
 ** remember to do a full re-index after adding code
 ** check the wp_facetwp_index table if needed to see what values are being indexed
 **/

add_filter( 'facetwp_index_row', function( $params, $class ) {
	if ( 'my_facet' == $params['facet_name'] ) { // change my_facet to name of your facet
		$related_post_id = $params['facet_value']; // depnding on how your relationship field saves its data this might need to be changed or looked up from a different value
		$params['facet_display_value'] = get_post_meta( $related_post_id, 'some_custom_field', true ); // lookup custom field 
		$params['facet_value'] = $params['facet_display_value'];
	}
	return $params;
}, 10, 2 );

There's now an official add-on that we've collaborated with FacetWP on:
https://github.com/FacetWP/facetwp-pods

It covers relationship fields and all other pod fields :)