Every displacement hull has a theoretical max speed in which no matter how much power you throw at it, the boat will not go any faster.
I've read about it a couple times. And I can't explain it in detail. But the physics behind it has to do with the wave the bow creates in front of the boat. The more horsepower you throw at it, the larger the bow wave gets and pushes back against the force of the motor. Think of it like a train trying to climb a hill, except the more power the engine has, the steeper the hill gets, and the speed of the train will never go faster than a certain limit. The bow wave is like the hill, and the displacement hull can never climb over it, no matter how much power, because the wave just keeps getting bigger.
Here's the hard part to grasp for me. There's a mathematical formula for this, and the max speed is proportional to the length of the hull. The larger the hull, for displacement hulls, the faster that max speed is. Unfortunately, the longer the hull, the more the boat weighs, and the more horsepower you need for both the weight and the speed. There becomes a practical limit, such as in the case of an aircraft carrier, where there's a practical limit to the size of the engine.
Back to the pontoon boat and the question at hand on weather a 50 or 90 is best. Just pointing out there's a max speed that no matter how much engine you add, the speed will only increase by small increments. For displacement hulls that is. Planing hulls are able to climb over that bow hill, or wave, and then the boat speed increases as you add horsepower until you run into this same problem again, only next time it's with air resistance. More on that in a minute.
If someone can find the formula, you could calculate the theoretical max speed for a 22 or 24 foot pontoon boat with a displacement hull. This also explains why at some point you are better spending your money on a hull that planes up, and then go back to adding horsepower.
Doubt any of that helps much. 90 hp might be that point. Maybe 70 hp. Explains why you never see a 150 on a twin round pontoon with no strakes.
The wind resistance limit shows up in the speed numbers when you compare some of the top speeds of similar boats on this forum when one has a 250 and another has a 350. Top speed doesn't increase much for that additional 100 hp. Until you climb over the "air resistance" hill/wave. At which time, you'd be in outer space.