Fascinating question, and a topic I've often questioned.
There are two things that should be noted examining "Kunoichi" (くノ一):
– First, it's written with one character from each of the three writing systems in Japan:
–– Ku (く) is written in Hiragana
–– No (ノ) is written in Katakana
–– Ichi (一) is written in Kanji
At first blush we can say that this is literally an ideogrammatic representation of the kanji for woman (女) being largely the strokes broken up. We can ascribe meaning to this by saying that it's a count, that it deals with numbers, whether of orifices or people ( "ku no ichi" would better be translated as one of nine, and given the ninja's propensity toward turning women against powerful men, it might be in reference to the number of women a powerful man could trust).
The second thing to consider is that the ninja would create codes, and it's likely that Kunoichi is simply one of those codes, literally meaning "woman" – One code in Iga history was the combining of particles to create characters with different meanings. What looked like gibberish scrawled on a wall to one, might have a distinct meaning to a ninja. In some cases, breaking apart a character (kanji) into its strokes could conceal the meaning.
I would like to find the origin of the term in some text – Bansenshukai, Ninpiden, or the like to get a better feel. If we know the habits of the region of origin better, we might have better insight into the reasoning behind the word.
To expand upon PBJ – 忍者 are the characters "shinobi" and "mono" in native kun'yomi reading. In the Sino-Japanese (on'yomi) they are "nin" and "jya". In historical documents (Bansenshukai, Ninpiden, Shoninki, etc.) it's usually accepted to read 忍者 as "Shinobi no mono", or otherwise interpret 忍 as shino(bi).
More often than not, the terms used to refer to those people we commonly now call Ninja were colloquialisms – "Grass" (Kusa), or "One from Iga" (Iga-mono) were common for referring to Iga 忍者 as a whole. Groups such as the Fuuma were also known as "ruffians" (rappa). A common misconception is that the term Nokizaru (Macaque on the roof) was a general reference to the ninja, but this is not true. Rather, they were a particular group led by Uesugi Kenshin, Daimyou of Echigo Province.