If FDev wanted to create persistent clouds, it shouldn't be that hard to do so (performance issues aside) using the same seed that generates the surface topography.
Personally, I'd say clouds are something where anything's better than nothing.
By way of comparison, it's kind of like how our ships creak and rattle as we're flying down to a planet's surface.
Ideally, the amount of creaking and rattling might be related to how steep our descent it, how thick the atmosphere is, what our control imputs are and how laden our ship is.
That'd be the ideal implementation but it's sufficient to just have a bit of creaking and rattling thrown in as we descend.
Similar thing with clouds, IMO.
Generate the clouds using the seed for the planet's topography, put some water-droplet effects on our canopies as we're passing through them and have the ships buffet around a little bit too.
In terms of gameplay, it might actually have been a good idea to add clouds at the same time exobiology arrived in order to make locating stuff on a planet's surface a bit more challenging.
Course, now we have exobiology - but don't have clouds - there are probably people who've got used to finding stuff on a planet's surface easily (sometimes even tinkering with their gfx settings to help) and earn billions of credits and they'd moan if the arrival of clouds made their lives harder.
