Ex MK Pirates CM here.
The clouds have been present and switched on for several years now. The problem is two-fold. The boxes that generate the cloud projections are what we call ten-by-tens, meaning they cover an area ten foot square. The back of these have a very handy dimmer switch on them, and they aren't very tight, I'm afraid. Then 10x10s are some of the most reliable pieces of equipment in WDW, because Yale Gracey was amazing, so they don't get checked very often and the two projectors which create the clouds you speak of have been very dim for about 3-4 years now.
The other problem is that MK Pirates has never gotten a complete top to bottom lighting redesign. What's been operating in MK since 2006 has been a very quick patch job on the original 1973 lighting scheme. LED lights randomly co-exist with original theatrical lights and the whole thing is a huge mess running on 2 different systems.
As a result Pirates at MK has huge light leaks everywhere, and the result is that areas that are supposed to be in almost total darkness now have other lights leaking into them. This is due to the 2006 refurbishment which was a total botch. I don't mean artistically in terms of the Jack Sparrow stuff, although that's debatable, I mean there were teams trying to do work that others would undo... it was a huge mess. Anyway, the projectors have been up there grinding away this whole time but due to light leaks they've been all but invisible. Top of my wish list for this refurb is a totally re-thought lighting and sound grid. It would make a gigantic difference.
The rain effect you speak of has been operating intermittently. It's actually done with a disco ball. During one of the emergency refurbishments last year WDI was able to get all of equipment for the Hurricane Lagoon show scene refurbished and tuned up. After the refurb the rain was working great, and they even re-painted the lightning bolts! I haven't been on PotC much since then, so I can't speak for lately. If the rain effect is out for refurbishment, it could take a very long time for it to return. These devices are going on 45 years old and they're unique one of a kind analogue effects. When WED and MAPO were folded together in the late 80s a lot of Yale's original effect boxes were made essentially obsolete, so when they have to be serviced, often times parts must be manufactured to get them working again. They're really beautiful pieces of mechanical engineering.
Disneyland replaced nearly all of their Yale Pirates effect projections with digital projections back in 2006. I think they look lousy, but that's me. The few that still are original is the group of clouds above the chase scene, which are from back in 1967. They aren't housed in projector boxes like the MK clouds are, they're just a pocket spotlight shining through a rotating disc exactly like a Christmas tree light. Oh, and the clouds/moonlight effect in the Blue Bayou, that one dates back to the 1964 World's Fair.
