A tarp or something could help to cover your cargo, but honestly that will add wind noise. If I were in your position, I would bite the bullet and get a cargo box so that everything is contained in one unit, covered, and won't add as much wind noise. Also, you never know if rain or other conditions will ruin your roof-mounted cargo.
"Why would I want to profess my feelings for some 3D girl?" - Tomoya Aki from the anime Saekano