Aye ... and personally I think that the "spawn chance" for new lairs should increase as lairs get destroyed.
(not immediately, of course, but the longer time passes without new lairs being spawned, the greater the chance increases)
So for instance ... you could avidly destroy all the lairs, and only have to deal with new lairs one at a time, maybe once every 10 turns (and thats if you control the world/ world-wide) ...
Yet ... the more that time passes, eventually the lair spawn rate will increase until a "reasonable number" has been achieved.
New lairs shouldn't technically spawn new monsters right away ... so even if you were keeping up with killing lairs, and then suddenly stopped, you would have a good 50 - 100 turns of relative safety from monsters. (they'd still spawn "guardian lurkers" but nothing that would roam near civilization)
Of course, Cities that have nice Walls will pretty much not have to worry about most spawns ... as even bandits shouldn't be able to attack a City wall in low numbers/ lack of siege. Only powerful spawns will be a threat to cities during the late game.
You could almost think about such lairs as "instances" ... only they have a hefty recharge rate.
Obviously a percentage of these lairs could lead to nastier lairs, or simply (if failed attempt) an angry "Lair-Leader" that gathers an army of beasts and starts attacking cities/ resources.
Meanwhile, all these NPC adventurers keep spawning ... at the beginning of the game they would primarily spawn in the wilds, but slowly they would start spawning in Owned cities ... until almost all NPCs were "born" in a City. (they wouldn't belong to the city though, still NPCs).
These NPCs would go after the weaker lairs first (following their own AI agenda at a micro level), trying to level up and gather loot. Occasionally they might uncover a big-bad that they can't handle, and that's when the military has to get involved.
But the point is ... that the low-level lairs can (later on) be fully ignored by the Factions, and left for the spawning NPCs to take care of. Obviously, players CAN micro these things, or rather, they COULD select a party of heroes to travel to lair upon lair, in the name of loot and levels. But they don't have to.
Instead, they could just worry about them early-game, clear out as many near-by lairs as possible, build up their defenses, and forget about them (only dealing with rare and large spawns on the MACRO level).
