Aperture used to be like iPhoto – all the pictures you added were stored in its internal library, a single file which ring-fenced your shots from the outside world and enabled you to move your library around as a single object. You can still do that with the current version. It’s simple and secure, but as library sizes grow, increasingly impractical.
So Apple soon added the ability to reference external files. This separates the Aperture library from your original images, so it’s messier and more prone to user error, but perhaps the only long-term solution to ever-growing image collections.
This is my setup. My Aperture library is in my Pictures folder, but my original files (‘Masters’) are on an external WD drive.
So that’s what you have to weigh up: managed vs referenced files in Aperture. It’s really important to know how both systems work, which one is best for you and, if you’ve not been paying attention, which system you’re actually using! Because until you know this, you won’t know where Aperture has put your photos…