Security vulnerabilities in well known web applications and technologies are a common attack vector. Keeping your web applications up to date can reduce your risk of being hacked significantly.
With more than 250 plugins that identify technologies removing the Powered By reference may not be enough to obscure the technology being used.
Once an attacker has fingerprinted the technologies in use they can then move onto to exploiting them. By testing your system you can re-mediate and keep your technologies updated.
The command line arguments used with the online Whatweb scan perform a passive analysis. For a full overview of the tool and the available options take a look at the project page.