I can see why "not knowing how it fell" can be a story point. (10,000 years is a LOOOOONG time)
I can see why "It had to fall for this story to happen" is a plot necessity, and can totally dig that.
However, things always happen for a reason. A society with advanced manufacturing, processing, and science-- does not just abandon those things. There HAS to be a reason. For the ancient puebloans, they ran out of water. Had to abandon their advanced civ. (well, advanced in a relative sense) For the Sheikah technomagical society? Maybe there was an internal conflict? Perhaps, after defeating Gannon, there was now a huge arsenal just sitting there, and then political inquiry on what to do with it, how to sequester it for later generations, and what to do with the people who have knowledge on how to construct such clearly dangerous instruments. Perhaps there was yet another falling out with the political establishment, which gave rise to the Yiga rebel group, which ultimately destroyed the civ through internal civil strife?
There are a number of plausible explanations, but no real cannon info to give a direction there.
As for windfish dream whales-- It lives on Koholint island, which you can find on the map in the far southeast of the map. Kakariko is much more inland, and high sheika society was evident all over hyrule, including up in the guerudo plateau. Rather far for a dream whale to be roaming free, unless there was a massive infestation.