Centuries-long wars and the absurd number of pillagings happen because of a combination of changes that happened during the population and sprawl rewrites:
a) Armies winning a siege against a site seldom ever destroy it, pillaging it instead. This happens even when the defending population of the site has been reduced to zero during or before the attack.
b) An entity can wage war against another every week, instead of every year as before the population rewrite.
Basically what happens is that after an attacking civilization kills off all of its enemy civilization's soldiers (which happens often because DF wars are almost always one-sided), the victors keep on attacking the now-defenseless sites. This can theoretically happen as often as every week.
It seems that the game has never had a concept of the end of the existence of a civilization except in terms of the destruction of its sites. In previous versions, when an entity became unable to defend its sites, it was "properly" annihilated because all of its sites were destroyed by invaders and turned into ruins. But because sites are only rarely destroyed in recent versions, the game can't know that the entity is essentially (from our point of view) eliminated, and so the other entities can't know to stop attacking them. After a certain time, these armies are just sieging and pillaging sites of civilizations whose citizens have been killed off long ago. It's as if 21st-century Greece still regularly sent its armies to attack Troy.
The system is obviously borked (though surprisingly few people talk about this flaw), but I like to think of these pillaging expeditions as a ritualized march, a tradition desperately cherished by once-warmongering nations forever unable to come to terms with the era of peace in which it finds itself.