How do these sites know what framework I'm using and how do I hide it?

I can confirm that these tools (among other indicators) use the default session cookie name as a method to determine what system is running a particular site. After changing this setting the known tools where unable to determine codeigniter on my project.

Code:

$config['sess_cookie_name'] = 'ci_session';

But apart from that every thing you leave default (in output to webbrowser) can be used to identify the system, for example a default generated 404 error, some directly accessable file (some default css file for example) or a non deleted welcome page could be used as fingerprints to determine it.