Hermione never stepped out to try and have a turn, she is not even mentioned in the book the whole time the others are dueling the boggart. I guess the boggart never rolled in front of her and Lupin thus never had the chance to give her a go with it in the first place. And after he stopped Harry he probably wanted to finish it off since most people had their turn and so that Harry won't have an other one. I don't think he thought of Hermione for a second.
Anyway during their DADA exam in the end of the third year they have to duel the boggart and Hermione sees McGonagall telling her that she's failed all the exams.