I don't think there is any explanation given for why the storm came about. I admit I didn't really consider the possibility that it is the one that swept Ciri's parents away. But while the timeline could allow for this, as Season of Storms is set somewhere between the stories from The Last Wish and Sword of Destiny, I had the impression that the storm
Vilgefortz caused near the Skellige Isles
was of a much more local nature, rather than a huge tsunami that buried an entire kingdom. I didn't gather that this was suggested to be the same storm.
Even more so, I think there might not necessarily be an explanation for this storm. The storm derives its significance largely from the fact that it is not only a fitting finale for the story, but even more so a fitting end to the city/kingdom of Kerack.
Throughout the novel, we hear about the city's decadence, the arrogance of its leadership (I think we're told the mayor basically just declared himself king at some point and everyone went by with it, or something like that), as well as the mess of political intrigues among them. It is really not a nice place (yet you could probably say that about a lot of places in the world of The Witcher, which tends to paint politics in a generally cynical light). Adding to this, we even hear about the city not existing for many a while longer very early on in the story.
Now all this adds to the fact, that I think the reasons for this storm are to be sought more in the metaphysical realm than anywhere else. If you call it the "wrath of god", the course of history, or simply fate, it was an end deserving to this city. The murder of the king and the usurpation of the throne during the wedding is one part of the city's downfall and the storm is its finalization. It is analogous to many a classic tale of a city devoured by its own decadence in form of a seemingly natural desaster, be that Atlantis, Pompei, etc.
All this is to say that I think, yet again in a Sapkowski novel, the reason for the storm is left deliberately ambiguous as part of an ending more to be taken for its narrative and thematic value than to be questioned for its true background.