The issue I'd like to clarify is included in the title of the post. I've noticed that in MT 5.0 in "settingtypes.txt" file cloud_height isn't referenced anymore. What's more, in Win64 version the command "/set cloud_height <value>" does seem to be acceptable as the game returns answer "cloud_height=<value>" (however with no ensuing change in the actual clouds height) which in turn isn't true in the Win32 version (the same command fails when it's issued).
Does it mean that this setting isn't maintained in the newer versions of MT? I highly doubt it, I'd suspect that it was rather overlooked and should stay as an important world parameter.