From what I can tell, it definitely requires editing of the main module (or rather cloning it and editing it under a different name to avoid any issues) which would mean it would only function with a new save or a ported save (which requires some editing of a file iIrc).
The "moods" and "day settings" are set via atmosphere settings and triggers, they are local. One atmosphere per map file which is a "default state" and then there are triggers which alter it, so when you leave e.g. Cyseal, you will walk into a trigger which changes the atmosphere to e.g. dark and rainy.
Now, the problem is: To create a day night mod, one would have to have at least two triggers per location and a timer and
some way to exchange said triggers on the go.
One trigger, which is in place during the day and moves away if a certain amount of time passes so that the night trigger can replace it. Then, one would have to tweak the transition times (not sure how to go about moving them and doing that, didn't work a lot with the toolset yet) to create a smooth transition from day to night. And it's not even said that two atmosphere triggers would be enough per environment. Eventually, one would need another one for morning and one for evening too.
Now, if what I said makes any sense to anybody or is in any way correct (this was solely based on a quick analysis and assumption on how the system works in the Divinity Engine), this would be the reason why.
I'm very sure it could be done with code (creating a special atmosphere trigger with day, night and morning/evening settings for example), but we simply lack any documentation on how to program stuff properly for usage in the game and it's all a trial and error process what most (including me regarding the editor and own modules) do with the given toolset.
It will take a while until we will get official tutorials on such stuff, I guess. Until then, we will have to continue experimenting and helping out each other with own tutorials.
But I can assure you, it was thought of. I'm pretty sure it will be just a matter of time until we have proper tutorials and modding skills to pull that off.