I think Manon's short hair is because she is a convict rather than being unhealthy (although she is that, too) and as such has had it cut that way prior to being put on the boat. Perhaps partly as a health consideration considering the (presumably) cramped and dirty conditions on board the boat. All the women convicts have had their hair cut that way.
I think the ballet is all the better for it as it is only increases the contrast to the Manon of the previous two acts. She is almost unrecognizable and that is precisely the point IMHO. Of all the dancers I've seen take on this role (most notably Guillem and Rojo) they seem to relish the opportunity to dance/act such a role that is so real, unforgiving, emotionally devastating and well, 'raw'.
(plus she still gets to have nice hair, frocks, jewelry, money, fur coat, admirers, a carriage in the other two acts!)