Not true hiding, but pretty darn close.

This is not a documented feature so expect this to vanish at any point. Adding this should be considered experimental at best.

There may be times that you need to hide a page from your Shopify sitemap. To do this you just need to add a metafield to that object – pretty simple stuff really – especially if you’re using ShopifyFD to manage your metafields. No app or expert required, so feel free to DIY.

This is the property you’d add:

metafield:{"namespace": "seo","key": "hidden","value": 1,"value_type": "integer"}

Easy right? I’ll probably just add this as a dedicated button within ShopifyFD to save having to manually enter it each time. Once that’s set you can also add some liquid into your theme files to check whether to add a no-index meta tag as well:

{% if product.metafields.seo.hidden == 1 %}
<meta name="robots" content="noindex">
{% endif %}

Now don't be a fool and start adding this to everything in site. Screwing up a stores ability to have products (for example) appear in sitemaps is not something you should take lightly. If you add this to a clients store you must tell them you did it, and how they can remove it. There will be nothing in the interface that will make it clear this metafield has been set so it can be very easily forgotten.

If you want to set the metafield via the Shopify Admin for products you can use this magical link: Load SEO Metafields in Shopify Admin. It will jump to the bulk editor with the metafield settings ready to use.

Update 1: Looks like there's now an offical doc page for it over at Shopify. Unlinked from the main docs, but it's there.

Update 2: The new version of ShopifyFD now adds a button to add the metafield for you automatically on products. See below.