I believe the rivets are packaged by weight. I know that's how they're bought. It makes more sense for Van's just to come up with an approximate weight amount, with some extra thrown in, than to count each and every rivet in a kit. By the time you get to the end, yes, all that extra has built up.
I know that I still have a bunch of AN426AD3-3.5 rivets, which makes sense since they're the most used on the kit.