There are multiple reasons for invading armies to destroy settlements and either kill or enslave population instead of ruling over it. They all depend on strategic situation and type of the warfare an army is applying.
If we take Mongols as extremely prominent example, it’s easy to see they considered cities and villages as vital points of enemy infrastructure and tried to kill or at the very least disperse civilians in order to instil fear and deny their enemy supplies and mobilisation reserves. Mongols utilised terror of the total war to their advantage by killing and pillaging as far as they could, making the remaining enemies flee and taking their possessions with less resistance.
An army participating in border warfare could very well be engaging in destructive raids in order to wear down enemy forces and probe their defences. A raiding party may find it cumbersome to take prisoners and spoils of war with them in case they’re afraid their adversaries can catch up with them. Yet the enemy lines are ought to be broken and his positions weakened, that’s why they would exterminate population and pillage settlements as that simply is faster to do.
Examples of such behaviour are abundantly throughout Eastern Europe where big battles in medieval and Renaissance times were relatively rare, but small scale raiding warfare wasn’t. Due to big distances between towns it was important to field as many horse raiders as possible to disrupt enemy communications, and high speed of these squads meant they could strike, easily prey on defenceless populace and retreat, evading repercussion. Such pattern was common for the Croat divisions during The Thirty Years wars. They became a literal bane of the German pastoral centres during their expeditions. Same can be said about wars of Russia, Poland and Lithuania. During Russo-Swedish war of 1591-1595 it was common for both sides to engage in mutual raiding on the far north, exterminating locals and capturing goods of the enemy merchants.
At the very least, such violent behaviour was common in case an army enraged by enemy resistance loses discipline: Italian mercenary companies in 14th century were especially notorious for this, it wasn’t uncommon for them to start robbing the town they swore to protect if the town in question is late with payment.
Sometimes it's because the goal isn't conquest. Chevauchee had a different intent, as u/sunagainstgold examines in this post, as well as u/Rittermeister in examining a raid here.