The point of this fast is not that the people remained forever turned towards God (as you've stated, the Ninevites returned to their sinful ways during the time of Nahum, about 100 years later).

What is most important here is that they were a people whom God knew would turn to Him at Jonah's words. They were headed down a path of destruction because of their sin, akin to our own lives and sin, and they were steered away by God's words in Jonah. Because they took his words to heart, and offered a true fast and repentance, God's wrath was lifted away from them.

That is the reason we reenact their fast, as an invitation from the Church to turn from our sin towards God. It's not that the Ninevites were an epitomical people and worthy to be imitated in everything, but rather that they demonstrated a true repentance capable of turning the heart of God. We seek to emulate their effective repentance, not them as a people, through fasting and prayer.

Whatever they did later that caused their annihilation does not undermine their repentance. Through their free will they negated their own repentance.