On my class C, there is a rubber gasket between the bunk board and the roof of the chassis cab, which seals it against water getting inside. (The screws that attach the two to each other are driven through the gasket.). You can't really see the gasket from the outside, and from the inside it's normally covered by the headliner trim.
I don't think any caulking etc. is going to make a bit of difference in terms of wind drag, at least that could be measured in terms of fuel mileage. It might very well eliminate some annoying wind noises if they are coming from that area.