One thing I’ve noticed about the new FCP is that it wants you to do all your media management within the program. The way I organize by client is simply to create a new event for each client; that way I don’t have to display the clips from other clients when working on one. If ever there is a client with such sensitive data that I don’t even want other clients seeing the name of the event, I’ll dedicate a hard drive to that client (not uncommon in my workflow anyway, given the large amount of storage needed for some of them). However, I have yet to have a client that was that concerned about confidentiality. Even ones with NDAs surrounding our work don’t really care about the name of the project (although naming it by the client and not the project itself would be another way to get around this).
Anyway, where I was going with all that is that I’ve stopped worrying so much about how the media is organized on the drive. I still create client folders, but mainly to house graphics files (.psd, .ae, etc.) and other resources that may not be directly used within FCP.
Of course, you could always house your footage in nested folders and simply have links to it in your event.