And Apple apps don't go to great lengths to hide photos. They are stored in your Pictures folder in a package e.g. Aperture Library. Just right click and your photos are there. Packages are great for inexperienced users since it is easier to backup and less opportunities to mess up the metadata.
Aperture and iPhoto use same library DB packages now, and Aperture's a cheap upgrade if you've outgrown iPhoto's consumer family interface. Aperture lets your organize any way you want, to any depth, with nesting of any kind within any kind.
And the metadata is stored inside the iPhoto/Aperture library package. For Aperture at least it is an open standard XML file so there is no 'lock in' what so ever.
And even Finder quicklook seem to render the full .jpegs just fine and fast enough, so wasting so much disk space on a useless preview/thumbnail feature (to me) is a dealbreaker. I'd even be willing to accept missing or postage stamped thumbnails, rather than having to uninstall applications and remove music to make room for my photos.
Split across different folders depending on whether you have edited them or not.
Other enthusiast friends of mine hate the package approach because they're very used to the file management approach, so YMMV.