Even when the sky appears uniform to our eyes, it isn't. The index of refraction of air is affected by a number of things (e.g. the shimmering mirages you see over a hot road) - temperature, humidity, turbulence, pollution, density due to elevation, and probably others - especially at boundaries where one or more of these change rapidly. In addition, just because you don't see a white puffy cloud doesn't mean there aren't areas where there is a higher concentration of water vapor or ice crystals that just aren't dense enough for our eyes to detect them. These, along with sensor noise of various types, dirt/oil on lenses, and even the differences in algorithms used to process the sensor data, can all lead to what looks to be a uniform sky being actually very non-uniform, although the differences are all in the low-order bits of the image (i.e. they're small). Algorithms such as unsharp masking have a tendency to exaggerate these small differences, as you've noticed. You can use various forms of blurring to make those small differences disappear again, but probably at the expense of some additional image clarity elsewhere.

In other words, this really isn't something you should be concerned about. As long as your final images look good (i.e. you haven't boosted that non-uniformity too much), you should just ignore this, because it's normal.