I think the following might work?
from sqlalchemy import func
session.query(Order.user_id,
func.count(Order.user_id)).group_by(Order.user_id)
Anyway a little more is to be found here:
http://www.sqlalchemy.org/docs/ormtutorial.html#counting
http://www.sqlalchemy.org/docs/reference/orm/query.html#sqlalchemy.orm.query.Query.group_by
Lance