Everything we make has some flex. Buildings flex, airplanes, bridges, huge ocean ships, and even our C-Dory boats. My 93 does exactly what you guys are describing.
But, the "fix" is very simple as all you have to do is slow down to the speed where it doesn't do it anymore. Our boats do not run through sloppy chop at high speeds very well at all. And once you get that through your head and adjust your actions by reducing your speed, this flexing will become a distant memory. I have no idea what happens if you just ignore it and let the pounding continue. But my intuition tells me it just isn't good.
Others have suggested adding stiffeners and you can. It probably will help. However, the engineers that design things take into account the natural oscillations that ocurr while cars, boats, trains, and planes have while in operation and adding stiffeners may add a problem somewhere else.
Unless you have a serious hull problem, and I doubt that you do, I would just slow down. If you can't just slow down, I think you maybe you should be looking at a deep-v boat as they deal with the chop much better.