How to hide Magento from CMS detectors?

First you need to know, how your website is identifiable as magento, as there are a big number of possible proves.

• basic html structure
• magento specifiv css
• special js code on product views (assuming you already obfuscate the js files)
• some routes special for magento
• headers and html head
• some file locations usually accessible (licence file, skin path, /js path)
• API endpoints

In the end the better question is, how much work do you want to invest, and if it is worth the work.
In case of security, there are enough blind attack bots out there, which trys magento attacks on your website, even if it is not recognizable as magento