When I fly up to the clouds, I get to the height of the clouds and the wings just stop making me fly. I glide back down to the ground and can't get back up. I can occasionally get past the clouds but its extremely hard and most of the time I end up dying before I get past the clouds.

I don't think this is intentional as you said the wings only have 2 drawbacks: wings and armour. There's also not a setting to disable this or change the height at which they stop working

I also noticed that the setting for the flight speed doesn't work: I change the value but I still go the same speed as before.