No, you shouldn't shoot into the sun or any bright light source with any stereo stereo camera. But a camera with modern lens coatings will handle it better. Lens flare almost always ruins a stereo image.
As for the square format, in stereo, the frame almost becomes irrelevant when looking at a stereo image in high magnification. Really, stereo photography is almost like another medium, compared to mono photography. Traditional composition rules don't really apply.
In my opinion, 6 x 6 is the best possible stereo format since it is the largest format for which a simple backlit Brewster-style stereo viewer can be made. If you go larger, you will need a more complicated (larger and heavier) viewer with mirrors. That type of viewer will have to be custom made. It will also be challenging to mount stereo images and align them correctly in such a viewer.
If you really hate square format for stereo (I would be surprised if you feel this way after seeing a stereo slide in a handheld viewer), then you can still use a Sputnik and crop the image down to 6x4.5, which will improve the image quality be cropping out the vignetted, soft corners of the frame.
I believe all mass-produced medium format stereo cameras have a square format.