It is important to distinguish between "the first Version" and "the last remaining Version". Aperture doesn't privilege in any way "the first Version", but it does, in a very important way, "the last remaining Version". Please see Frank's excellent User Tip for a brief explanation.
For me, this was an important reason to always use Adjustment Stacks, and to store and develop Images in Projects, but to prepare for publication, and publish Images in Albums
Message was edited by: Kirby Krieger -- clarification added.
Deleting the "first" version is the same as deleting the "second" version if you have two versions. No difference; the original image will still be in your librayr.
If you delete them both, your photo will be moved to the Aperture trash. If you then delete the Aperture trash, the photo will be moved to the OS X trash. If you then empty that trash, your image is gone, and unless you have a backup, it's gone forever. If you have a vault, then the next time you update the vault (if the image was in the vault) the backup will be moved to the Vault (deleted images) folder.
So it's really hard if you have a reasonable backup plan to unintentionally delete master photos. But people still manage to do it somehow :-/