I checked out the S&S scripts, and they don't change weather, except for a single script run (fraction of a second) to simulate a lightning flash, before setting it back to what it was before. So S&S can't be responsible for weather changes.
Regarding interior sounds and whatnot, S&S only uses PlaySound(3D), so it's not responsible for stopping interior sounds. However, its sounds aren't set to loop, so depending on script conditions it may only play them once (creating interior sounds for a couple of seconds), and then stop (leaving a relative silence).
So S&S can't affect AN's workings, and it is possible that S&S may only play interior sounds once of its own accord. Hence, if you're getting the sounds turning off bug, I'd recommend that you disable the interior sounds part of S&S, and just use AN's sounds for interiors.
Now that I've cleared that up, I think that's all the weather issues sorted.