If they are solid rivets that have been peened, they are called "bucking rivets". The tool used to hit them, and keep the round shape is called a "bucking tool". Check out McMaster-Carr. They'll have what I'm talking about. If you can't get to both sides of the rivet, you could use pop rivets that are called "sealing blind rivets". McMaster-Carr don't allow you to link to their products, so you'll have to do a search.
I wouldn't use silicone. Use a product like 3M 5200.
Also, check out the Iboats forums. Lots of people/threads pertaining to this, with plenty pictures. Good luck!