What's the point of destroying ghoul nests?
Solution 1:
In addition to repopulation in a very few areas (as mentioned by Aegis), you also get experience points and looting them yields materials. The bombs regenerate when you meditate, so for me it's an easy choice.
Solution 2:
Some areas where the ghoul nests are will become repopulated with people again once the nests are cleared out. You'll know this because a cutscene will trigger with people returning to that area.
Solution 3:
If you're in it for achievements, there's one linked to destroying all the monster nests in a region.