Is it possible to hide certain entries in the Content SEO section of SEO Matic?
A Section only appear in Content SEO if it has public URLs. If it has public URLs, that means that Google and users will be able to find it eventually.

There is a setting to disable the sitemap for a section via Content SEO, however.

Can you elaborate on what you're trying to accomplish?

Also we got into detail on sitemaps for a while on the devMode.fm episode SEO for Web Developers: The Silence of the Chickens which might be useful to you.