Quick Question, were ninja still active during WW2? If not, when did they stop being utilized? If so, any accounts worth sharing?
There is no evidence to support the ninja being active much further than the Edo Period. Fujita Seiko was claimed to have taught ninjutsu at Rikugun Nakano Gakko (Nakano School for Military Intelligence), but there's no evidence to support these claims.
Essentially, the historical record of the shinobi ends with the Shimabara Rebellion (1637-1638). "Men from Kōga" were employed by Tokugawa Iemitsu to steal into and survey Hara Castle.
There are similarities between the ninja and the Oniwabanshu (Garden Keepers – the secret intelligence service of Tokugawa Yoshimune in the early 18th century); however, there is no evidence from contemporary records naming the Oniwabanshu as shinobi.
Edit: A Last Account of Shinobi
Unfortunately, I can't effectively corroborate this story. It was told to me by a friend after he visited the Iga Ninja Museum in Iga-Ueno, while explaining a picture of a document in, if I recall correctly, Portuguese.
Toward the end of the Momoyama Period, Japan began to close itself off. Before the Portuguese were effectively kicked out of Japan following the Shimabara Rebellion, a small cadre of shinobi were sent onto a ship to steal what was believed to be important documents proving espionage. Supposedly, since none of the agents could read Portuguese, what they came back with was a hand written document in Portuguese that amounted to a bawdy poem.
Supposedly, this was considered a complete disgrace, and signaled the beginning of the end for the shinobi as reliable agents.
Actually, Yes they were... Although they played a fractional role, Ninja were active in both World Wars. There are several 'odd' accounts of US servicemen being attacked and 'taken away' at night on many of the islands where they were stranded and where fighting took place. I read a particular interesting account (partial account actually) where a US naval serviceman was taken at night and woke several hours later quite a 'long distance' into the jungle (unaware how that could have occurred) from their beach encampment (these were survivors of a ship that struck an underwater mine). This serviceman was supposedly tortured (mostly by hand) by a single individual for some time (torture would certainly make time pass 'very' slowly..) and then surprisingly, abandoned once this small group (his assumption) found out he was not the person that they had sought out (also his assumption due to specific questions being asked of him). This serviceman was always 'alone' while being tortured and the face of his attacker WAS shown to him. The man however was blindfolded whenever anyone other than the sole 'torturer' was present at their own camp.
What I get from this is that the Ninja were not particularly 'worried' about what the individual would say or do while in their custody nor once released as they did not 'kill him'. I would assume that the 'Ninja' is now no longer used due to the advent of high tech warfare and CCD camera's etc, (difficult to hide from those), but soft targets may be a 'different thing' and I would imagine they could still be useful for abductions and similar things...
I don't think there is a consensus on the definition of shinobi/ninja, and thus their existence at any given time is spurious.