With Blue marble, yes . I can't confirm now, but I think it is some option called cloud coverage ( in BM interface, that is )
P.S I remembered now: changing the clouds was not directly in Blue marble, but on CivScale. CivScale, as you probably know, was discontinued by Coldfever due to the defective interaction of changing the relevant files with the actual result in game.
It should be easy to do with some XML editing, though.
P.S 2 I gave a look to the game files in my laptop and saw this in Assets\XML\Art\CIV4ArtDefines_Misc.XML
Code:
<MiscArtInfo>
<Type>ART_GLOBEVIEW_CLOUD_SHADOWS</Type>
<Path>Art/Terrain/Sky/Clouds01decal.dds</Path>
<fScale>1.0</fScale>
<NIF>None</NIF>
<KFM>None</KFM>
</MiscArtInfo>
<MiscArtInfo>
<Type>ART_GLOBEVIEW_CLOUDS</Type>
<Path>Art/Terrain/Sky/Clouds01.dds</Path>
<fScale>1.0</fScale>
<NIF>None</NIF>
<KFM>None</KFM>
</MiscArtInfo>
I think this is what you are looking for.