Where I see two images of the same photo, I imagine these are actual duplicates-am I correct?
Not necessarily. Edited versions will be stacked, if you have enabled the general preference "Automatically stack new versions", but you still may have created unstacked versions that will show as unstacked.
If the image is a duplicate, how do I know it is a duplicate rather than a version of the photo? I simply want to be sure I'm deleting dupes and not Master Versions.
By default Aperture will add a version number to the version name, e.g. "P1260567 - Version 2". A sure test to see if similar looking images are versions of the same image, is to drag one of them to another project. If it are true duplicates, only one of the images will move, but if they are versions of the same image, both will move to the other project, if you drag one of them.
OH and maybe I should also confirm: are stacks of one image only or a series of images one might have taken on the same day?
The Preferences allow you to automatically stack new versions, but you can also stack bracketed shots and time series automatically - see the paragraph "Creating Stacks" in the User Manual: Creating Stacks
Or you can stack images manually by selecting arbitrary images and using the command "Stacks > Stack"