There are two cases of blowpipe-wielding hunter-gatherers being made use of in modern jungle warfare: the Dayaks in Borneo during WWII, and the Orang Asli (Senoi/Temiar) in peninsular Malaysia during the Malayan Emergency, the post-WWII conflict between the Malayan Communists and the British colonial power.
On the first, see this link to a PBS program called The Airmen and the Headhunters, based on a book by the same title by Judith Heimann.
Mainly told by Dan Illerich, the last surviving airman; the original Dayaks who protected the Americans; and the Australian commandoes who helped get them out, the story transports viewers deep into the heart of Borneo at the height of the Second World War revealing fantastic tales of survival, bravery and ingenuity. The Dayaks, who hated the Japanese for occupying their country and killing their beloved missionaries, hid the Americans deep in the jungle. When the Japanese soldiers approached from the coast, the tribesmen used blowpipes and the banned practice of headhunting to stop their advances. They even set up an ambush using naked women as bait, and once the killing was over, invited the Americans to a rare headhunting feast.
The clash of cultures didn’t stop there. Months after the airmen went down, they were found by British Major Tom Harrisson and his group of Australian commandoes, who had been tasked with setting up a guerilla army to attack the Japanese from the interior. Harrisson enlisted the Dayaks to fight, encouraged headhunting and the use of blowpipes against the Japanese, and concocted a daring plan to build a runway out of bamboo so that planes (and their very brave pilots) could land in the jungle and take the Americans home—which they eventually did.
Source: The Airmen and the Headhunters
See also Heimann’s fascinating biography of Harrisson, The Most Offending Soul Alive.
On the second, see John D. Leary, Violence and the Dream People: The Orang Asli in the Malayan Emergency, 1948-1960. Leary fought on the British side during the Emergency, and his major thesis is that anthropologists who paint a picture of Senoi culture as inherently non-violent have it all wrong. He relates numerous cases of unprovoked violence, even massacres, on the part of the Senoi during the conflict (where both sides were attempting to secure their allegiance.) For example:
Leary himself presents an example of their capability to kill as based on evidence in the travelogue by Richard Noone (appointed Advisor on Aborigines by the British Forces in 1953) and Dennis Holman Rape of the Dream People (1972). These authors ventured into Temiar country during the Emergency in search of Richard’s missing brother Pat, a military officer appointed the first Protector of Aborigines, until an eyewitness told them that he had been shot with a dart from a blowpipe by a jealous indigenous blood-brother in an argument about Pat’s Temiar wife.
Source: Review of Leary by C.M.I. van der Sluys in Bijdragen tot de Taal-, Land- en Volkenkunde (1996), available on JSTOR.
Edit: There is also the Senoi Praaq, a unit of the Malaysian police. According to one book about them (R. Jumper, Death Waits in the Dark: The Senoi Praaq, Malaysia's Killer Elite), they use blowguns as well as more conventional weapons. Wikipedia:
Though the Senoi Praaq troopers were given a choice of weapons, they
reportedly enjoyed scoring kills using their traditional weapons - the
blowpipe being a favorite. They particularly enjoyed a leisurely hunt
that would take a few days, stalking their prey as if they were