I think it is a cloud issue. Me and a squaddie both flew through a dense cloud on climb out, icons were all there before we entered and all icons stayed gone for both of us when we exited. We all noticed immediately. The rest of the squad couldn't see our icons either after the cloud but could before. I ended up exiting the game and reupping which fixed the issue.
My uneducated guess is the game doesn't register that you exited a certain type of cloud and keeps the icon settings as if you were still in it. Basically you're permanently hiding in a cloud.