Not necessarily, it would depend on the type of warfare waged. Typically, medieval warfare tended to fall apart into two categories: the siege or the chévauchée. The former obviously targeted specific spots, often cities or key fortifications. But these were costly and hit or miss efforts.

Quite often, warfare would be about plunder & rapine. This was what we call the chévauchée, basically a large-scale raid seeking as much booty as possible. This type of warfare accomplished two goals, the first already mentioned, namely loot. The second was nevertheless also important, namely displaying the ineptitude of the defendant. This is why the English embarked on the famous chévauchées of the HYW: it showed that the Valois were weak & that the blatant failure to defend their lands from the ravages of the English, was an admittance that god favoured one side over the other, that legitimacy was on the side of the Plantagenets. This was a characteristic of medieval conflict resolution, endemically featuring at the lowest feudal echelons, but taken to the level of states and all the horrors of war that ensued.

So, on these types of campaigns, you can be sure they scoured the land for those villages all the same.