It makes sense to me that gas may not go through a filter once it is wet with water. I have done a lot of filtrations in lab where I'm running an organic solvent such as gasoline through a filter paper with no problem. Once the filter paper gets wet with an aqueous solution such as water then organic solvent will not readily pass through the paper if the 2 liquids are immiscible. The water coats the paper and the organic liquid just doesn't go through (unless some pressure is applied to either push or suck the liquids through the paper). So, if the filter contains some kind of high density pleated fiber then I can understand water blocking the filter. If the filter is just some kind of coarse mesh plastic then I don't see that water is going to "plug up" a filter.
All I know is that I'm going to empty every fuel tank on every engine I have and make sure that things are clean and dry before winter sets in. Generator, weed eater, lawn mower, tractor, chain saw, pressure washer....