I am far, far from an expert, but I have built 3 canopies all which used water-based stain covered with polyurathane and have not had any problems with cracking due to heat. Of course the oldest one of these is only 3 years old, so perhaps for very long term use, the issue might arise.
I believe I have heard of folks using oil based stains (and paints for that matter) with a good sealing coat on top, but I don't have any direct experience.
Just my .02
Good luck