There are window-material manufacturers who suggest you can use windshield wipers directly on their windows’ surface without scratching. First, I have always been concerned that over time, and with salt water, the windows will scratch. Second, because of the stiffness, if you snap them up while running, the bouncing can crack them.
My suggestion is to have wipers inserted into the forward window material. If you look at the boats in your marina, you will probably see this style of installation. I would also suggest you use whole pieces of a hard material — hopefully coated with a totally scratch-resistant glass material, with windshield wipers installed — and if you want the enclosure open, store the pieces. Finally, you can go with a true glass section that is either not temporarily removable or that is stored. Talk to your local Bimini installers, and after a few visits and quotes, you will find out what is best for your application.