Aha, that makes a lot of sense. It's a shame, because I always enjoyed being so high up I could look down on the clouds, but it's understandable because otherwise that would be incredibly hard to code. :\
Well, they aren't realistic, and they make it harder to see.
When I took a single engine plane up with my flight instuctor to practice intrument flying, when we got up into the Cumulouse clouds, (Not only could I not see ****) The entire cockpit fogged up, so minecraft was already realisitic, clouds seep into things.