For record: It looks like this topic really interests some people: http://markmail.org/message/nic7xrgf5uzed5c4
Newport was obviously thinking in the same direction:
They offer an option to use SketchUp and provide 3D models of their mechanics and lenses—at least they used to, since this page does not exist anymore and the picture above was kindly sent to me by Newport to answer the request in the comment.
Having background in both optical engineering and experimental optics, I can say that real experiments and setups are usually designed with a piece of paper if they are simple or with the professional software if they are not. Real systems very quickly stop being a bunch of mirrors. This is, probably, why nobody is seriously considering creation of such a tool.
In labs, we are usually trying to align all beams parallel or under 90 degrees to each other---not only for ease of work but also because otherwise polarisation effects start being a problem.