I noticed that helicopters are usually placed right on the helideck but sometimes they are depicted flying over the ship. I'd guess the latter case is for ships that do not have a hangar, is it correct? In general, is there some kind of rules or guidance on placing helicopters?
Place em on the landing spot. If a ship can house more than one, place one on the landing spot, have the other in the air, at the roughly same height as the missiles. It's not a hard rule, but it's what I usually do.
If a ship can have lots of helos (or planes, like carrier), go wild. But not insane