There are ways around all internet filters, and most of these take less than a few seconds to initiate. It just takes a little bit of knowledge of how the internet and computers work. The government line is, "its all to protect the children from pedaphiles, and the country from terrorists and extremists", people buy this line because they are fearfull, and ignorant of how the internet works. Terrorists and pedaphiles are already using alternative means to accomplish their agenda, they already know how to bypass any government filters or traps.
As for EMP, yes, it could take out large parts of the internet temporarily, and yes, this would cause chaos. It is an indiscriminate means of destruction, so if TPTB did this, it would be cutting their noses off to spite their faces.
A far more effective way of dealing with any websites that promote conspiacy theories, and are considered subversive to TPTB, is to simply use a very successfull propaganda technique, and label all these sites as the internet loony bin. This they have done with great success already. Some of these sites are the loony bin of the internet, and do have an overblown sense of their own importance, and think they 'know' the 'truth', some of these sites actually do know the 'truth', but lumping them altogether removes credibility from all these sites, regardless of individual credibility.
In the case of the website 'whatreallyhappened', I think it is a case of them trying to promote their own agenda, by playing into people's sense of drama. In other words "we must be important because the government is blocking access to our site", when quite clearly this is not the case.