The motors are different- they both just happen to be 800s for marketing reasons. The transmissions have different ratios, the shaft drives have different ratios- they have nothing in common except the brand name.
The S50 is a very light bike with torque and very steep gearing for rapid acceleration. It also has a lot of lean angle, and because it is so small and light it is a blast to toss around in tight corners. It has been on the market since 1992 (previously named the Intruder 800) so there are a ton of aftermarket accessories for it. In a drag race or in the twisties, the S50 blows the M50 away like it is chained to a tree. Chances are Suzuki wil cancel the S50 in the next year or two, as the styling dates to the early 1980s (when it came out as the Intruder 700) and it does not sell very well anymore. But they are a blast to ride, and very reliable- I went 135,000 miles on one, and have 75,000+ on another.
The M50 is a sportier version of the C50, with an almost identical engine to the C50 in the same frame, but with inverted forks and agressive styling. It is a more modern design with fuel injection and modern styling. The heavier, larger design makes it ride smoother and be more comfortable for taller riders. It looks like a current model muscle bike, not an antique chopper, so it will probably be with us for a while. Many aftermarket parts are shared with the C50, Suzuki's best selling cruiser, so there are no problems there.
The two bikes are so radically different that most people like one and hate the other. I love the S50's performance, but wish it had tubeless tires and was a bit longer and more comforable. I like the syling of the M50, but wish is had about 50% more horsepower so its performance matched its styling. I can live with the tubes and added highway pegs to stretch out my legs, so I can adapt the S50, but the lack of power on the M50 is a dealbreaker, so it is not on the list of bikes I would consider.