Ayu's not that bad off stat wise. Her BMI is 17.6.
Japanese cutoff for normal BMI is 18.5. She's underweight.
The Japanese have been steadily increasing in
height (graph II-2-1, page 6). (Original document is
here.) So, for 1999 values (when the game was originally released), she may not be that short. Also, you also need to know the parents' data to comment on her height.
Personally, I think that Shiori represents the average female teen height circa 1999, but I can't find alot of data to support this. Sorry.
For everbody heights...
Nayuki: 164 cm (5' 6")
Mai: 167 cm (5' 7")
Shiori: 157 cm (5' 2")
Makoto: 159 cm (5' 3")
Ayu: 154 cm (5' 0")