Scads and Scads of posts on the rivet vs. screw debate in the forum so I'll pass on adding to it.
However, if I read you right you're contemplating on, if you go the screw route, of glassing over the screw heads. Mostly for appearance I think. Personally, trailers being the fairly flexible things they are, I would want access to almost any fastener I installed for potential replacement without having to drill through gelcoat. Threads strip, or get cross threaded, or gummed up.
I may have misinterpreted your comment. In that case....Nevermind!