I am very familiar with this show and this infamous scene, otherwise known as "Two Idiots, one keyboard", and feel confident in stating that it is not self parody. We can arrive at this conclusion easily enough by acknowledging that they never had before, nor since engaged in self parody when thwarting off a cyber attack, thus why would they have in that scene. Parody also had to have something to actually parody, and there is nothing else going on to actually parody. There is no other scene that they are referring to, to thus make it into a parody.
I would suggest that four things happened to make this scene happen. One, they wanted to show how awesome the cyber attacker was by them being able to defeat both Abby and McGee at the same time. (Worf Effect) Two, the set designer did not have the time nor feel the need to find a second keyboard, something that would also dictate having a second monitor as well. (McGee's involvement could have been improvised on the spot when filming) Three, the director clearly wanted them both in the shot together, and this is all the setup allowed for. Four, Gibbs of course solves the problem by unplugging the computer (or at least the monitor), which is probably all they really cared about, showing how Gibbs low tech is superior to their high tech.