Finally found a way to get clouds working!
I exchanged the GWX scene.DAT file with the SH3 stock one. Than i edited all campaign .MIS files and put the following stock values in:
[Mission]
Title=GWXR1.02FULL
MissionType=0
MissionDataType=1
Year=1939
Month=1
Day=1
Hour=12
Minute=0
Fog=0
FogRand=0
Clouds=0
CloudsRand=0
Precip=0
PrecipRand=0
WindHeading=0
WindSpeed=5.000000
WindRand=0
WeatherRndInterval=5
SeaType=0
Briefing=
I launched the game through SH3Commander 2.7 and set Partial Clouds in SH3 Weather Gen 1.5. Went into my career, when it loaded, i clicked external view and there they were! I think i'll give it a test drive tonight.