Aperture can add a watermark file to an image on export but you have to prepare the file outside of Aperture in a program capable of creating a file with an alpha channel.
Most users find it easier to use a plugin for this and the plugin of choice seems to br BorderFX a free plugin that besides adding watermarks to images is capable of doing a lot more.
In addition it is capable fo working as both an export plugin and and edit plugin. The distinction being when used as an export plugin the image in Aperture is not altered the additions are only seen in the exported version.
As an edit plugin the changes made are saved back to the Aperture library.