Enemy ships will, friendly will not. If that's what your asking.

Are the ones that disappear subs?

I've noticed it with different room types, but not so much with inconsistency in the room.
Basically, GB2 seems to still have the ship on the mini-map, while select mode and old-fashioned regular battles obscure that as well. Haven't tried blitz or night battle lately.

More or less yes OjamaPeter

The plane is hiiiiiigggghhh above the smoke, so when the smoke is launched, there is noway to know where the ship is(you cannot hear them over your LOUD engine).
If one of your ship's FCS is in sight range, you'll still get the dot because although you cannot see, you can hear the enemy ship.
(Although it means the enemy ship is toast, as there are ways to know EXACTLY where they are even when they are in smoke *cough*moving your screen so the red blip is at the edge and firing there*cough*)