I was the smallest kid in class up until about my freshman year. Even until I graduated I was small. People always thought I was younger than I was and my parents even made me lie about my age and eat off the kids' menu up until I was around 16 (how mortifying!) It sucked, back then, but I did mature, eventually, and I suppose it probably kept me out of trouble...for a time (I didn't drink or party until I went to college. How can you get away with underage drinking when you look 12??) But, the good news is, that I think I have remained "young looking" even until now. I often get comments that people don't think I look my age. Perhaps your daughter has that same sort of "trait" that will carry into her older years. If so, she will be thankful.
Also, (and yeah, it is probably way too early to approach this benefit of smallness) if she turns out to be a girl who doesn't date boys who are shorter than her, she will have a larger selection to choose from.