Hacking the NSA website is not hacking the NSA. Hacking a website is relatively easy and not that interesting to people who deal with servers day-to-day.
Well, more to the point, it doesn't imply anything about the business end of the agency's systems being compromised. If you hacked into the actual CIA or NSA as in having similar access to an authenticated agent, that would be quite bad for them. Taking down their website is something they don't really care about.
Right, see. When you say "Relatively easy" do you mean: "it is just subtly easier that compromising the NSA itself" or: "I'm surprised it doesn't happen every day"
The point isn't whether its easier or harder to deface a website. The point is that a public facing website is a more or less static advertisement for an organization (like a poster), thus taking it or even the server that hosts it down doesn't impact the operations of the organization in any meaningful way.