Question: Bats and Whales, and some monsters like the Hook Horror, have blindsight based on hearing. You can tell it's based on hearing because they also have the Echolocation trait that says their blindsight does not work if they are deafened. For the purpose of this discussion, please assume a totally dark environment.

Beyond the range of their blindsight, these creatures can use their mundane hearing to detect other creatures, and they can benefit from Keen Hearing, giving them advantage on Perception checks that rely on hearing. Within range of their blindsight, what changes? Do they still benefit from Keen Hearing? And how does blindsight change what they can perceive over and above mundane hearing?

In particular, to what extent can they pinpoint the exact position of creatures within and outside the range of their blindsight?

Answer: 
RAW, Keen Hearing and Blindsight do not in any way work together or "stack". They are both used completely independently of each other. It does not require there to be "a completely dark room" to interpret the rules:

* Within the range of the blindsight the creature can use blindsight to "see" and and can use wis(per) rolls with advantage from the Keen Hearing just the same as any other creature with Keen Hearing (e.g. attempting to hear whispers well enough to understand what is being said)
* Outside the range of the blindsight the creature has no benefit from blindsight and can use wis(per) rolls with advantage just the same as any other creature with Keen Hearing (e.g. attempting to hear if anything is stealthily approaching)

The other senses of the creature operate as usual for the circumstances.
If the creature they want to target is outside their blindsight range and *not* hidden, they can target them with disadvantage from being blinded. This is not something particular to Keen Hearing, anyone can do this.

You appear to be making a mistake in thinking that if a creature cannot be seen then the default state is their location is unknown - in fact the default is the opposite: the location of a creature is known *unless* they are hiding. See [What advantages does hiding have?](https://rpg.stackexchange.com/questions/63441/what-advantages-does-hiding-have/63453#63453)

If they are hiding then Keen Hearing allows advantage on the Wisdom (Perception) check to beat their Dexterity (Stealth) check. Normally, this is passive versus active so advantage gives a +5 but if the perceiver wants to spend an action they can make an active check.