I imagine the biggest problem with clouds is duplicating the exact extents of their ephemeral nature across multiple clients in MP.
Sure, I would like them to look as good as possible, but what I care about MOST is...if that cloud is blocking my view of that escort but not the bomber he's escorting, while the escort does not see the same cloud and has a clear view of me... I'm playing with "clear skies" from now on. No second thoughts.
Clouds are either blocking LOS in the same way/location for all units on the map or they're actually hindering the gameplay by giving me or my adversary an unequal advantage over the other.
While I freely admit this has to be a NASTY thing to code well, I can't be accepting of que sera sera. It works like it needs to, or it can just go away.
In fact, didn't Strike Fighters have that very issue so TK removed weather from MP, you only saw clouds in SP?