I'm pretty sure S&S is compatible, because I seem to remember using it at some stage, and I've been using All Natural for ages now.
By the way, as aellis said, you can certainly use Natural Habitats in combination with, well, just about anything (AN included). I do!
With default settings, All Natural combines the weather from Natural Weather, Enhanced Weather (another good mod in its own right, btw) and Atmospheric Weather System (I think...) - but you can choose any one, or any combo of two, if preferred. There are a number of other interesting ini settings to play with too, like replicating "Darker Nights" or whatever that mod was called, or setting your own tweaks for how dark nights are, and whether they have the default Oblivion blue tint. And so on.
Oh, and a number of spectacular mods exist that depend on AN. Immersive Interiors, for example.