I mean, even today water spouts are pretty fuckin' crazy to look at. What did people a thousand years ago think about them? Punishment of their god(s)? 'Just' nature?
I can't imagine any pre-basic-scientific-knowledge person being able to understand how something like a tornado or water spout could ever be 'natural'.
There's always room for discussion, but perhaps the section How did earlier civilisations deal with hurricanes and tornadoes? in our FAQ will answer your inquiery.