We know the story history likes to go with, at least. But I know that the idea of the "great fire that killed everyone in it" could solely be myths perpetuated by Kyoto nobles when they saw it happen (Kyoto was pretty close to the site, no doubt it would look violent.)
I read somewhere (In Nobunaga no Chef, loll) that an archeological dig had been conducted where they found that there were no skeletal remains or a "strata of burnt earth from the period, as would be expected."
-- And that there supposedly weren't many people on the mountain at the time. (Which makes sense to me.)
Although I'm assuming any articles/books where I could read more about this would be in Japanese and hard for me to find.
I'm convinced already that a large part of what people think happened on Mt. Hiei was exaggerated (probably because that's what Nobunaga wanted people to think, when he razed the temples) but are there more sources that go in-depth into this? Whether books by Japanese authors or western authors, or... even any helpful articles online?
The archeology article was written by Kaneyasu Yasuaki in 1981, published in the Shiga Archeological Journal volume 1. The article's titled "Archeological Re-examination of Oda Nobunaga's Burning and Killing of Mount Hiei."
Or in Japanese: 兼康保明. 1981. 「織田信長比叡山焼打ちの考古学的再検討」『滋賀考古学論叢』第1集.
I haven't read it myself, but it's mentioned in various works. They found only the main hall and a few of the surrounding buildings to have clear evidence of destruction to the time. Burnt earth could be found in other places but they do not date to the time period. Few artifacts could be found from the time period as well, most finds dating to prior periods or from the Edo. Note the dig wasn't over the entire mountain, just the East Pagoda, West Pagoda, and Yokokawa areas.
Kaneyasu's conclusion is that 1) at the time the monks left at Mount Hiei had mostly moved to the Sakamoto (foot of the mountain) area, where most of the fighting likely took place (note Kaneyasu's dig did not include the Sakamoto area) and 2) burning the entire mountain and everything on it is a great exaggeration.
Kanyasu's 1980 dig report (no focus on Nobunaga, just the general dig) can be found here.
Moving to primary sources, the relevant passages in the Chronicles of Lord Nobunaga is here. It speaks of the soldiers burning the foot of the mountain and then moving up to the top. Monks, women, and children were killed, more captured but then executed. The death count is "thousands". A translation is available online if you have access to Brill through an academic login. Google Books partial preview here.
A Japanese translation of Jesuit Luis' Frois' letter describing the event can be found here. According to Frois due to years of warfare the mountain had fallen from a height of 3,800 buildings to just 400. The letter time the event beginning on September 29 at the villages in Sakamoto at the move the mountain, and on the following day attacking the main halls on the mountain top. Frois give 400 buildings burnt. The death count he gives is "about 1,500" men, women, and children. In his "History of Japan" on my shelf, the number given is "1,120 monks who took up arms" against Nobunaga.
The Dai Nihon Shiryō gives the relevant passages from various monastic and aristocratic diaries starting here. Some say the entire temple complex including many buildings of the East and West Pagoda areas (which according to Kaneyasu's report the damage found was fairly limited to the areas of the main halls of each) was burnt. Others only mention the main halls, as those were the most important. The Diaries of the Overseer of Kyōto's Tō-ji Temple gives the most concrete count, with Konponchūdō (East Pagoda area's main hall) and 16 other pagoda and towers, and the homes in Hachiōji, Torii, and Sakamoto.
Many of the diaries do not give a concrete number for the deathtoll. The highest death count is found in Yamashina Tokitsugu's diaries, at "3~4,000 men, women, and children, temple and lay." The Nendaiki Shōsetsu (Copied Stanzas of Chronicles) says 1,600. The Records of Kyōmonbō says "about [a] thousand heads taken." Kyōto's Tō-ji Temple Death Register is the lowest, at "hundreds dead."
I really don't know where Stephen Turnbull (cited in wikipedia) gets "the final casualty list probably topped 20,000." Even the Picture Book Taikōki, which is Late Edo historical fiction, about as unreliable as you can get from a source, gives "3,000 of the temple monasteries killed or ran away."
On the other hand, I want to be very clear. We should not take this as a numbers' genocide olympics. A massacre did happen. Whether the death toll is hundreds, a thousand, 1,5001,600, or 34,000, the event greatly shook its contemporaries.