I am sure if you Google
it, you will find a variety of filing systems, including waterproof ones, but they will all take up space on your boat
Have you considered gradually converting them all to PDF's and storing them on your computer or tablet? Most of the manuals
you are likely to have on the boat are available as pdf downloads, and most are free.
Once on your computer, it is also much easier to search for a given item, using "Find", "Spotlight" etc.
- just a thought