By what? It's impossible for a process to know for sure if the system is rooted or not. A rooted system can present itself to a process to look like a non-rooted system if it's engineered well enough.

I'd bet that most of these apps probably just check if "su" returns a shell, in which case perhaps all that's needed is to modify the "su" executable to require "su --magic-phrase foobar" before it drops into a root shell, and returns "bash: su: not found" or whatever if called with no arguments.