Monotouch compiles the app into the native code. How can Apple know that the app was built using MonoTouch? Does Monotouch leaves a signature in the application?
Does Monotouch has its own libraries which could be a trace of the origin or it compiles all the code and all its .NET libraries into native code?
The resulting .app package contains the application binary, your resources as well as the required additional libraries, such as:
As such, it would be trivial for them to check if the application was built with monotouch or not – it is as simple as right clicking the package and then select “Show package contents” in Finder.
However, you need not worry about that, as Apple has just relaxed their License Agreement: http://daringfireball.net/2010/09/app_store_guidelines