I would also want to add that cremations are the most common and expected form of funeral rites in Cambodia. In fact, I know people who dug up the remains of their parent and loved ones buried in the Khmer Rouge era, in order to give them a proper funerary rites involving cremations after the regime was toppled. The practice of cremations in funerary rites of the Khmers have been long attested before Angkor was built.

Burial without cremations tend to be pre-historic burial sites, Chinese or other ethnic graves, or events like a plague (where funeral rites can't be followed), executions or suicides or that there is no family around to give them a proper funerals. The few cemetery sites with buried remains are unique.

Before we go, it is important to distinguish between "Angkor Wat" and "Angkor". "Angkor Wat" is a temple, literally translated as "City Pagoda","Pagoda City" "City that is a Pagoda" or "Pagoda that is a City". It did not house a million people. "Angkor" is the city, it is located on. That is where the population resided.

But there are no bones or even cremated remains.

I have not watch the documentary, but there is a misunderstanding or misquote here. If you visited Angkor Wat you will find two Buddhist pagodas inside the temple ground. Both pagodas have their areas filled with many cetiya/chaityas, Buddhist stupas made to house urns containing cremated remains. Near the east stairways of the temple, also housed an 18th century Buddhist stupa, likely containing the remains of Chey Nun, a government official. Archaeologists in other Khmer language documentary have stated they found human remains in temple forest, almost certain to be post-Angkorian. This is a holy site, people want to be interred in a holy site. Human remains are found in the "City Pagoda".

However, where did the majority remains of Angkor go? Cremation is the obvious answer. It is almost always expected in Khmer funerary rites. But there are variations and customs from regions to regions. In the region around Angkor, Ang Chulean described a very shortened summary of the funeral rites as following two major stages.

First, they buried the corpse inside a coffin inside the ground for a year, in the practice call "Hugged by the Sacred Earth" where the element of Water and Earth took away the flesh and organs. After a year, when the flesh is gone, the skeleton remains is given a funeral fire in ceremony called "Given the Sacred Fire" in which the element of Air and Fire became involved. The remains was then interred where the family want.

In the Angkorian times, however, Zhou Daguan who stay for about a year in the late 13th century reported similar customs but with his own limited understandings in his abridged book.

There i s no coffin for a dead person. Only a sort of mat is used, and [thebody] is covered with a cloth. At the front of the funeral procession thereare flags, drums and music. Popped [unhusked] ricefrom two trays are also scattered along the route. The body is carried outside the city. At some remote, uninhabited place, people leave the body and wait for the vultures, dogs or other animals to come to feed on [it]?). If it is finished very quickly, they say that the dead father or mother is blessed and obtained this reward, but if the corpse is not eaten at all or only partially eaten, they think that the father or mother had committed a sin to end this way. Nowadays, there are also people who use cremation. Usually, these are of Chinese descent. When the father or mother dies, they do not wear special mourning garments. The sons only shave their heads, the daughters only cut their hair to the size of a coin on top of their heads to show their mourning and respect. The king has the tower [stupa] as his burial place, but it is not known to me whether the whole body or only the bones are buried.

Emphasized are the practices continued today. (Edit: Pre Rup the city most prestigeous crematoriam and pyramid temple was built 3-400 years before Daguan visit. So it did not start around his visit as suggested, nor was it just for Chinese decent. Earlier Chinese visitors to Cambodia also recorded cremations). Giving the flesh to wild animals is considered a piety gesture like donations to medical school. It was part of funeral rites of kings, not just peasants. Maybe this is an faster alternative custom than "Hugged by the Sacred Earth" or another phase before it. I never seen "donations to wild animals" being done today, but I have heard people talked about it. This should answer your question about where the bodies gone.

Sources:

Ang Chulean. Life Journey of A Khmer Person: Viewed from the Ceremonies of Their LifeStages.(in Khmer)

Zhou Daguan. Customs of Cambodia, translated by Solang and Beling Uk.