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Depending on how you read the whirlwind ability, it is either created by the air elemental "puffing itself outward and spinning in place" and the whole whirlwind is the body of the air elemental. (In which case it actually gets easier to hit it since there is a size increase involved.) Or else it involves the air elemental flying in circles really super fast (in which case putting an arrow into it just involves waiting for it to come around to your side, and then putting an arrow into it.)
I am leaning toward the latter interpretation as there is a PC class with the whirlwind power, and if the whirlwind did involve a shape and size change, that class would have to have had language about what happens to a PC's gear.