My answer will focus only on your first question: Can clouds be used as hiding places?
Yes, but not always, and not reliably, because...
Clouds don't last forever.
Cumulonimbus (thunderstorm) clouds build and then dissipate. If you're trying to hide yourself in one, sooner or later your camouflage will vanish from around you.
Thunderstorm clouds aren't fun to fly in
I'm a pilot, thunderstorms are Not Okay to fly in. In their official publications the FAA says things like:
...extremely hazardous...
...almost impossible to hold a constant altitude...
...attempting to maneuver greatly increases stresses...
...penetration of any thunderstorm can lead to an aircraft accident and fatalities...
What the...hail?
That's right! Thunderstorms also feature hail. Hailstones have killed sheep before. Sheep. If it can kill a sheep it can kill an eagle (or equivalent eagle-sized flying creature with hollow bones)
Depending on what latitude your story takes place in, there's also ice!
That's right, in the wintertime you won't get cumulonimbus clouds. Instead, you get to deal with freezing rain, which will form on the wings of your flying creatures, adding weight and hindering their ability to fly.