I would assume that females from shinobi clans would expect to join the "family" business, and this is somewhat supported by canon, although strong assertions can't be made. Inuzuka Tsume and Hana, and Yamanaka Ino are examples of this from Konoha that I can name off the top of my head.
Yet, every major battle that a kunoichi fights threatens her ability to have children. Certain poisons could make one sterile and certain direct blows to the abdomen would destroy any chance of having children, and I'm fairly sure they haven't invented IV fertilisation. Death, and worse, infertility, would be fates all too common for kunoichi. The path of the shinobi is one of death, and I would hardly expect most kunoichi to survive until retirement, let alone in a condition viable to have children.
Also, in order to have children, kunoichi would doubtless be forced to take leave, or retire. The changes in pregnancy, particularly in the third trimester, would be extremely dangerous for both the kunoichi and the child involved. Retiring would probably be a better option, considering that at least six to twelve months of inactivity would destroy the kunoichi's fighting ability.
So, the question remains why such numbers of kunoichi are existing in Konoha and the other elemental countries. It certainly can't all be attributed to blood lines and clans. Sure, some women don't want children, but in this world, CHILDREN are being shinobi, when they are unlikely to be mature enough to make such a decision about their lives.