If I'm understanding you correctly, what you are seeing is how every single deck hatch is attached to a deck - regardless of the manufacturer. There's no need for a washer under the screw head - it's useless. The only way to use nuts is to thru-bolt it but then you'd see it on the cabin side. So I'm not quite sure why you're asking about that?
If it hasn't been proactively sealed over the years, there is a risk that the core material is soft or even rotten. Inspect it - repair what you can and decide if it needs further attention. Reattach the everything just like you took it apart. Boat Life LifeSeal is excellent - 3M Silicone, as well. Stay FAR away from any heavy adhesive caulks like 3M 4200 or 5200. Butyl Rubber tape is an excellent material to use, as well. Tape around the hatch BEFORE you remove it to make cleanup easier.
