In short, the concept of kunoichis as seductress female ninjas is an entirely fictional invention.

In the Edo era (1603-1867), the word くノ一 (kunoichi) did not even mean female ninja - it was used as a rare alternative way to refer to women (女) in general. The meaning comes from the strokes in the character 女 (woman) - when handwritten in Japanese it is drawn with the 3 strokes くノ一, which when written separately can be read "kunoichi". So at the time period discussed, the word simply meant "woman".

However, its not specifically a movie trope - the word trope of female ninjas was popularised by the series of books known as the Ninpōchō series (忍法帖シリーズ) by Yamada Futaro (山田 風太郎) 1959-2001. This series depicts a number of fictional conflicts set in the Edo era, and features ninjas as we know them from fiction, using hidden weapons and seducing their enemies. Both the trope and the word kunoichi itself were popularised by the influence of the Ninpōchō series, which is the first known use of the word kunoichi to refer to female ninjas specifically.

As for what actually happened in the Edo era, as far as I know there is no reliable historical source detailing an actual example of kunoichi-style espionage.