Clouds like this:
are indeed possible using the terrain tools currently provided by ED.
One could create the clouds in 3D max and assign the shapes to a superficial overlay (areas like runways and taxiways use the superficial system). These render at 80+ km in the game and will blend into the scene from a distance.
Both top and bottom normals would then need to be assigned the cloud's texture. It would be preferable to assign the interior normal's (bottom normal's) texture as pure white or off white. The outer cloud shape (top normal) could be emphasized as a texture by doing a texture burn in 3D Max after unwrapping.
The only problem with this method is that as you get closer, the jagged geometry of the clouds would begin to show. However, this could be solved using packets of sprites in a secondary superficial overlay (sprites like the kind used for runway lights and city lights http://forums.eagle.ru/showpost.php?p=713217&postcount=10).
Note 1: this method will actually render true 3D clouds not just a ceiling with a texture (as described in the cloud creation procedure for stratus clouds below).
Note 2: If Eagle Dynamics were interested, they could use a fractal algorithm (http://www.outerra.com/wgallery.html) to solve the jagged cloud geometry problem which would eliminate the need for sprites.
Note 3: Placing clouds like the ones mentioned above would be feasible if they were placed over large bodies of water. This would be congruent with real world phenomena as clouds tend to gather over moist areas. The true advantage would be that the polygon count could remain lower as terrain and clouds would not have to both be rendered in the same scene. For instance if one were to construct a Hawaii terrain, it would be ideal to place these clouds in the expanses without islands.
Clouds like this:
are very easy, by comparison and can be created using a .tif of the cloud image and assigning it as a superficial overlay (see above) on the y and x plane. Again this can certainly be done using the current terrain tools.
Of course, these methods would take a lot of time to complete...probably why no one has done it thus far...