They weren't cloakers actually, they were darkmantles. Not sure why I felt OCD enough to correct that. Also, I'm not sure why WotC got brought into this. This was from the World's Largest Dungeon (3.5e) from AEG games. Totally 3rd party. Someone else mentioned WotC modules having the same sort of thing though.If a player has said they're scouting, I definitely give them Passive Perception vs stuff on the ceiling. If they say they're focused on the ceiling specifically then at least Advantage (or +5) to spot stuff on the ceiling, but Disadvantage (or -5) for stuff on walls & floor.
Re the cloakers though, if they are above the archway & drop the moment PCs enter the room, I can see why the WoTC adventure says auto Surprise unless PCs are specifically looking up. There are still ways to negate this, such as Alertness feat (can't be surprised) or Barbarian reflexes (rage & act while Surprised). And 5e Surprise doesn't necessarily give Advantage on its first attack, the cloaker still has to roll Stealth vs PC passive per. So it's not as unfair as it might appear IMO.
I once had a giant snake over a doorway drop on first PC entering - automatic Surprise - poor snake, the PC had Alertness, won Init, and killed the very surprised snake before it could even attack!
Like I said, things like what you're describing are things that bug me in a game. I'm looking around. My character has a pretty high perception score (or spot or whatever your system uses). If you say X you get bonus Y but penalty Z is a losing bet, most of the time. I mean, using your examples, why would I do that unless there was some reason I knew there were monsters hanging on the ceiling beforehand? It's just as likely that something will come up from the floor, so, it's a wash.
Actually, thinking about it, in 5e, there really aren't any monsters that hide on the floor particularly, so, why wouldn't players just always look up? Odds are they are going to be right more often than wrong. And since there's no bonus or penalty horizontally, it's a free advantage that works most of the time.
Thinking about it, that's why it bugs me so much. It's just so easy to game the system. Or rather, game the DM. And, frankly, often, DM's are not very good at judging odds. Like I said, there are far, far more things that drop on you in ambush in a dungeon than hide on the floor. So, unless there's something wonky about the floor - pools, water, watnot - you're far better off looking at the ceiling. Judge your DM. How often does he/she drop a pit trap in a hallway? Never? Great! Keep your eyes on the ceilings boys, free bonuses for everyone.