>Or did men teach this to women back then too, in a dojo setting?

The system has been relatively stable for a long time. The teachers, up until fairly recently, were overwhelmingly male. Naginatajutsu/kyujutsu would have been a subset of the curriculum of a kobudo, and the teachers would have been expected to know and teach across the curriculum, not just sections of it that women were expected to know. There would have been plenty of female practitioners and experienced students, but female teachers would be unusual, and much more so the higher in the hierarchy you went.