"However, some cookies are exempt from this requirement. Consent is not required if the cookie is: used for the sole purpose of carrying out the transmission of a communication, and strictly necessary in order for the provider of an information society service explicitly required by the user to provide that service." Source: http://ec.europa.eu/ipg/basics/legal/cookies/index_en.htm#se...
So it turns out the directive isn't as dumb as many believe it to be, but a lot of webmasters wrongly believe that any cookie usage implies having to put up the notice. (Or the nuance was lost on the in-house legal team who briefed the webmaster.)
I run a software-as-a-service company in the EU, but only use cookies for login management. Therefore, I do not need to use the warning. But if I would track my users for advertising etc. I'd have to insert the warning in my web app.
This thoughtless behaviour reminds me of the thousands of websites which include a "(c) YYYY" copyright notice in their footers, despite this being completely irrelevant in modern copyright law.