It's equally possible that GCHQ isn't sure that they aren't storing data (double negative, I know). Or that GCHQ wants to be sure nobody at the Guardian was savvy enough to sneak data on to these chips.
I'm not suggesting one or the other is more likely, I really wouldn't know. I find it more interesting that they felt the need to do this, when really the only assurance they have that the documents are destroyed is the word of the Guardian's employees. Other than someone speaking up, there's no way for anybody to actually know if there are other copies floating around.