Why were these phenomena (and the city of Troy itself) thought of as only myths, and what evidence led to them being accepted into historical canon? Are there any mythological phenomena currently that have mounting evidence towards their historical existence?
/u/KiwiHellenist has talked previously about how this is untrue and actually Troy was known to be real https://www.reddit.com/r/AskHistorians/comments/pr0xxc/are_there_other_historical_examples_of/
A core problem here is the term "myth," which easily conveys meaning in a way that likely did not apply to the story of the siege of Troy. Traditional European oral narratives tend(ed) to manifest as folktales or legends. Folktales (manifesting with various names in diverse languages) are/were stories told as fiction. Legends (also manifesting with various names in diverse languages) are/were stories told generally to be believed.
There are typically a wide spectrum of legends including etiological (stories about the origins of things usually in primordial or at least much earlier times), historical (stories about more recent events and people), and what are referred to with a number of terms, but let's agree to call them "testimonial legends." This last group of legends are accounts that people tell as occurring in the present or near present, serving as evidence that extraordinary things are possible (today, our urban legends fit into this slot).
When we consider ancient literature that seems to be reflecting contemporary oral narratives, we tend to group all of the evidence of stories under the term "myth." This creates a modern perception of those ancient stories that is not necessarily correct. There is an enormous difference separating an ancient account about how humanity came into existence from the story that Homer recounts about the Trojan War.
Modern Americans tell a story about George Washington chopping down a cherry tree and being forced into confession when asked about it by his father, because, Washington says, "I cannot tell a lie." This absurd story and the equally absurd quality bestowed upon Washington does not mean that Washington did not exist. The historical legend was told to be believed, but it is apparently false; Washington, however, was a real person.
Applying this standard to something like Troy and the Trojan war allows us to understand that the historical legend about the war must be understood as such: specific elements may or may not be true, but other elements may be verifiable in the historical and/or archaeological record.
That we can treat the "myth" of the Trojan war in this way, does not mean that other ancient Greek narratives that we group under the umbrella as "myth" can be regarded in the same way. Each story must be understood in its context, and it must be understood that not all the stories played the same role in ancient Greek contemporary oral traditions. The singular term "myth" generates profound misunderstandings.
I will continue this thread with an excerpt on the term "myth" from one of my books.
edit: thanks for the award!