For any given boat speed Turbos wouldn't add more stress on the hull than standard fins. But because they are more efficient, you wouldn't work as hard for that given speed. With Turbos you can make the boat go faster and accelerate better, so to that extent, it can put more stress on the hull.
Hobie considers a crack in the drivewell to be a defect, so in the unlikely event it happens to you, regardless of the fins you use, you get your boat replaced under warranty for 2 years. The hulls are built for Turbos, but if you have a defective hull, Turbos might help expose it sooner. If I had a defect, I'd want it to show up sooner than later for warranty purposes if for no other reason.
IMO, the benefits of Turbos far outweigh any potential additional risk of cracking the drivewell. Having used Turbos for 4 years now, I see benefits, not only in speed, but in range, handling tides and currents, powering through unexpected wind and chop, getting out of the way of some speedboat that doesn't see you, towing exhausted or disables kayaks or motorboats. In other words, they can extend your capabilities on the water and provide an additional margin of safety beyond standard fins. They're also more fun to use.
If Hobie were concerned about Turbofins cracking your kayak, no doubt they wouldn't be selling them.