If your users are using a newer version of Chrome (versions 90+), Heap will be able to render the heatmap correctly for websites that use a Shadow DOM.
Heatmaps uses static page content to create a background image, which presents challenges with the Shadow DOM, because in most cases a Shadow DOM is generated by Javascript after the page loads.
Google Chrome 90+ introduced the support for Declarative Shadow DOM, which makes it possible to capture the content snapshot including Shadow DOM without using Javascript.