As slaes pointed out, the procedure for making sure that the Joomla! strip will not cause problems is, simply, trial and error. That's why I don't generally recommend it; most users don't have the patience to go through this process. Besides, most fingerprinting attacks look at the generator tag, HTTP headers, and try to download extension XML and translation INI files.
For the first two, you can customize the output using Admin Tools. Use something funky, which will throw off fingerprinting scripts. If you take a look at the generator of this site you'll see that it's set to "IceTeaLemon" and the HTTP header is a geeky reference to caffeine ;) Direct access to extension XML and language INI files is automatically dealt with when you enable the front-end protection in .htaccess maker. That's adequate to block most fingerprinting attacks which are used by automated hacking scripts to "harvest" a list of potential Joomla! site targets before launching unattended hacking attempts.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!