Discussed here.
The thing to understand about agricultural societies is that you can get into a negative population cycle where a big loss of labor force means production drops and then population drops because of the decreased production and on and on.
So I would guess that the major impact of the Targaryens is that A. they killed a lot of people both in conventional warfare and by raining fire from the skies down on every major center of population over and over for nine years, and B. they caused a lot of damage to the productive infrastructure that the population centers were sitting on top of and depended upon.
To give a real world example: Genghis Khan’s destruction of the Khwarezmid Empire and the Abbassid Caliphate involved millions of deaths (both due to war, the Khan’s reprisals for his murdered messengers, and famine and disease caused by large-scale destruction of crops), but the real long-term damage was the destruction of the irrigation canals, which permanently reduced the agricultural productivity of the region.