Wow, 28! Hehe. Yes, this may be better handled with a cloud layer instead of the atmosphere. Still I'm not even sure why that would be causing such longer render times *in a particular area*. At 32 samples I could see it taking a while in general, but why that particular part of the mountain? What's there that's not everywhere else?
I will say that outputting all render elements like in your scene file will slow things down a bit and use more memory. I doubt you need all of them, so you might consider narrowing it down to the elements you're actually using.
Other than those two things there is nothing *immediately* obvious in your scene file that would be causing such a problem. But if you're aware of using a Reflective Shader anywhere but on the water (i.e. on the mountain somewhere, somehow), then reflectivity could be a contributing factor (I didn't see any such shader in that area though).