I think the key thing about using regular monster spawning (rather than nests) is that the spawning levels adjust based on the needs. It's quite clear that users want the ability to clear out areas if they want to. I suggest these rules, which are an expansion of what I originally mentioned:
1. In overland areas, the default spawning rate off screen should be moderate to low. The assumption is that it's open space, you're in the wild for the most part, so there's nothing blocking monsters from showing up.
2. However, if the player is making a concerted effort to wipe out mobs in the chunk, clearly the intention is to reduce the number of mobs, and that should be allowed to give a sense of accomplishment. In this case, it's as if the mobs are driven out of the area and spawning should be reduced to a minimum.
3. So long as there are other adjacent chunks that have not been cleared out (I don't mean entirely cleared out but mostly cleared out), monsters could occasionally spawn.
4. If a player chooses to empty out all the overland areas of a map tile, that's his choice. At that point I think spawn rate should be reduced to a trickle or perhaps even halted.
5. If there's an enemy presence of some sort (enemy tower, raging mobs, bosses, wind storm etc) the spawn rate should be higher, including in adjacent chunks. The idea being that it's more challenging to get to the boss fight since they encourage other evil beings.
6. Within buildings, spawn rates should be much lower than outside. Spawn rates in this case just simulate monsters moving around from one room to another, so clearing out a room essentially prevents monsters from spawning unless there's an entrance to another room that hasn't been cleared out -- then there's a chance that a monster will spawn.
7. Within caves, spawn rates should be higher than buildings but lower than outside. You can clear out caves but it's much harder since they're so big and branch so much. The same rules apply as buildings, so that if you wanted to you could clear out caves starting from the innermost cave and working outwards. It's just a lot of work that's not really justified -- they're caves, they're going to have enemies...
8. Over time, there's a good chance that rooms and caves will spawn monsters again. That means that if you warp to a cave you previously cleared that you haven't been to in several days of game time, it'll probably have monsters again. A cleared room has a smaller chance of spawning monsters over time, but it's still possible.
9. It'll be nice if overland areas that have been completely cleared stayed that way for a certain amount of time or for a number of turns or until some event happens in the macro game. The problem is that that encourages people to spend time clearing out overland areas. But then again, this game is supposed to enable people to pick what they want to do, so if they want to do that, why not?
I'm all for monster nests as macro-game entities that need to be taken care of. They could cause very high populations of monsters in the area.