The collapse of Adal in the North and Ajuraan in the South coincides with the abandonment of multiple cities such as the ones above, but also others like Nimmo, Hannassa, Nugaal Valley ruins, Mudun, Gondershe, etc both on the coast and in the interior.
This means the trade network that once sustained those stone cities was disrupted, and we know the Conquest of Abyssinia had a disastrous effect on both sides. If you combine this with the Oromo migrations, and the Portuguese blockade in the Indian Ocean, it makes sense why people slowly began to adapt the Somal lifestyle i.e Pastoralism, because it was less dependent on outside political factors when it came to survival and prosperity, and was only at the mercy of God’s natural laws.
What people don’t realise is that the Christians and Muslims in the Horn had a extremely lively trade that made both groups very rich to the point where one group had enough wealth to commission large religious monuments and buildings in the case of the Christians, while the other thrived with the construction of dozens of major stone cities all across Somalia in the case of the Muslims.
The Futuh was not meant to be a prolonged international war, but a swift conquest with a clear victor. The Portuguese prevented that from happening and therefore the trade routes that thrived before the war were never re-established. Many of the trade road cities that profited from that bustling commerce declined and were abandoned.
The once regional mother cities like Zeila, Berbera, Harar, Mogadishu, etc continued to stumble on with minor revivals here and there, but were shadows of their former selves. In this age of city-states that followed, the urban settlements that thrived the most were the smaller castle towns such as Qandala, Bardera, Alula, Afgoye, which catered more to the Pastoralist lifestyle (the Berbera fair is a good example) than the previously mixed urban / farming / pastoralist make up of the medieval period.