Don't know if anyone else had this issue, but when it rains and snows the sky is clear, there's no clouds where rain or snow could come from. It also never gets cloudy, it's just always clear. I use returner, tempest, register, saver, master controller, overwatch and errortrap. It really annoys me, as I don't want it to be sunny everyday. I changed some settings in returner, but none about clouds

Are you using any lighting mods? Or a custom world that might use its own lighting?
I think cloud cover is more of a pseudo-weather, as in it is present and varies even if you don't have the Seasons expansion. It sounds like you might have lighting in play that removed the cloud cover from those variations.

No I don't use any lighting mods and this happens in Starlight Shores it's also unchanged, I didn't download any routing fixes etc. I'm not sure if it happens in other saves or worlds, I'll need to check

It's possible it could be the Starlight Shores lighting, it's worth checking.
It could also be graphics settings based, if your game options are set very low it could be that clouds only render on higher settings.

I reinstalled my game and the problem seems to be gone. I also deleted some mods so they perhaps were the problem too. Guess the fix wasn't so complicated.