I'm not an expert, but there doesn't seem to be a lot of source material from the Edo period to say that kunoichi were well known (
more info from Japanese scholar). That being said, I wouldn't think it's impossible, just that it's not explicit that women did anything more than infiltrate households for the purpose of gathering information.
Broadly speaking, agree with you that women played various roles in the period beyond what is traditionally thought, whether approved by society or not. Good discussion on this
here. Japan during this period was definitely a patriarchal society and women had defined roles that were acceptable depending on social class, but there were deviations from the norm. This seems to be depicted well in the two episodes I've seen thus far, in my opinion.