First, the Aperture library is not a file, it is a special kind of folder known as a package. It contains folders and files, including a folder called Masters, which contains unedited master image files organized inside folders by year, month, and day. The basic idea behind a package is to keep end-users from accidentally mucking up the carefully-organized contents. If an end-user wants to make changes, it's important to use the tools/commands provided by the app.
The thing is, you can't assume all the photos you can view in Aperture are physically contained in the Aperture library. It's possible to "reference" image files that are located outside of the library. When you Import you have a choice where to Store Files: "In the Aperture Library," "In their current location," or in still other locations. What choice(s) did you make over the years? (If you're in doubt, there's a "Consolidate images for library..." feature that allows you to copy or move all images into the physical library.)
There is no particular reason you need to export images from the library, if your purpose is simply cataloging and storage. They're stored as well there as anywhere else, and databases (which is, fundamentally what Aperture is), excel at cataloging.
Export does not mean "remove" - Export is a standard Apple term that means, essentially, "make a copy of the file (in a particular format) for use outside of the app," very much like Save As... If you need to send someone a copy of the image, Export, and choose the appropriate parameters for the file you're exporting. You can export a copy of the edited image, or a copy of the unedited original.
Aperture contains a lot of powerful tools for managing your library, including the ability to split-off new libraries from the larger library (so, for example, you could archive a particular former client's work). Lots there, I'm just scratching the surface. Read the Help documents.