Joseph Linaschke, the Aperture Expert, has an excellent, very detailed explanation on what exactly happens when you empty the trash in Apple Aperture. The trash mechanism in Aperture can be complicated depending on what you are trying to trash: albums or projects, versions or master images, referenced or internally managed pictures. Joseph goes through all these possibilities and explains what happens when you actually empty the trash. Good reading and certainly helps avoiding mistakes which could lead to data loss.
In fact if the explanation is too detailed for you, check out the video included at the bottom of the blog post which explains the same thing.