It's unclear if this was a one-time scan or a recurring thing. Assuming the former, since they announced it ahead of time I would guess that anybody with half a brain would just delete any cheating tools until the upgrade was complete, then reinstall them.
Of course, this is all a moot point, as the online community predictably came unglued at the idea of a program scanning their hard drives and uploading data of its choice to a company's servers. The idea was apparently announced on Tuesday and was very, very dead by Wednesday afternoon. Apparently the thought of an invasion of privacy is even stronger than Everquest addiction. Who'd have thought anything was stronger than Everquest addiction?