I know this is an older post, but I'm now doing my fairings and I just match drilled those holes between the fuselage skin and wing.
My issue/question is about the fit of the overlapping skins. my fuselage skin hangs about 1/8" lower than the wing bottom, and clecoing the skins together of course causes major rippling because of the curved surface. I'm thinking about adding a filler strip between the skins just to make a clean joint, but if it is indeed structural - that would not be the best solution.
Also, if it is structural - the whole method of drilling those holes is very poor: You pre-mark lines along the wing skin and then you are supposed to take a stab at finding those holes in the wing by measuring off of those lines and back 3". Far from a good match drill. I had just enough room to squeeze in a hole duplicator, and made good matching holes, but the geometry of the two skins makes pretty bad ripples. Kind of a tradeoff between structure and aerodynamics for me anyway.
I sent my question in to Van's this am, I'll update when I get their comments.
picture of my wing/fuselage joint.