I disagree with the premise, there seems no reason to involve Anakin at that point in time. I haven't seen ATOC since it was in the theatres but wasn't there a line where someone said only a Jedi Master had access to change the files? If that was the case, it seems it would need the personal involvement of Palpatine, but only after he became chancilor (unless he was using Sith power).
That said, I woudn't put it past Lucas to get boy Anakin involved where he doesn't belong. Too bad he wouldn't do something cool, like a renegade Slicer group in the employ of Sideous.
Padawans are usually kept under close reigns by their Masters at the Temple. Anakin even more so. He is supposedly the Chosen One and they would be watching him closely because of this. So no I do not believe he is the one who erased the computer files. More likely the work of a jedi slicer(as suggested by my esteemed brother) or another such as Mace Windu or Count Dooku.