If the weather running in Lua can spawn lightning bolts, there’s nothing to prevent it spawning other things like puddles of water (or at the worst case, an invisible and temporary Wet Stone); which would be a very CPU-cheap way of representing runoff or flooding.
The weather system already does hook up to most of the rest of the game though – it affects hearthling behaviour, town visuals, the environment, and it interacts with buildings so players can directly influence how weather effects (or ideally doesn’t negatively effect at all) their town.
I would say that if weather is “half baked” it’s only in so much as the whole game can only be “half baked” at the moment; it would be nice to have some more features but the game isn’t ready to support them just yet. After all, we don’t have a fully simulated water system yet (we have static ponds and we can make rivers, but the game can’t handle generating them itself) so we can’t have a weather-based water cycle. We have some weather-driven effects on the hearthlings already and there are probably more which could be implemented right now, but the balance and feel of such effects still needs to be tested so it makes sense to introduce some now, test for a bit, and adjust as needed.