Hiding the WordPress CMS shouldn’t affect the SEO from your website.
All the main URLs should remain unchanged. Only the vulnerable URLs are changed once you change the paths.
Through sitemap.xml Google is notified about the new paths and next time the Google will verify the website it will index the new media paths together with the old paths.
We have tested Hide My WP Ghost on many websites and we noticed even a slight improvement in the loading speed and great results in search engines like Google, Bing and Yandex.