Hum. Big question.
I'am inclined to treat it the way Bash does it.
With a "Variable" boost. First, as you said, sometimes, the changing effects are purely cosmectic. And second, the way the damage system works in Supers fits better the way Variable option is used in Bash. Either you shoot explosive arrows or piercing ones, the damage is unmodified in Supers. Therefore, something like Super Weaponry (special bow) 4D [Boost: Variable - various arrows 1D] could do the trick, I guess. Maybe, in the case of explosive arrows, you would have to add an Area boost, but I don't know how to do it. Would it be a boost inside another boost?
Sorry for my English, but it's not my primary language.