Aperture can make a watermark on export. Then they are outside Aperture. I've done it. It works but it doesn't work as cleanly as it could have.

What makes this handy is that it keeps your files in your library and projects. So instead of sending out exported duplicates and then trying to put them back in manually, you're handling the watermarked images just like any roundtrip image to Photoshop or a filter. Saves a load of time building a digital gallery of your selects from a project. Couple that with a little Smart Filter sorting and it's the solution that should have come within Aperture but didn't in 3.