To start with he line of sight rules in the DMG talk about this specifically. If a line from one corner of the square you are on has a clear line to a corner of a square the enemy is on then both of you can see each other. If it doesn't then niether of you can see each other. There is no situation with a solid obstacle where only one of the parties has line of sight according to those rules. Now I would not rule that way with a character trying to hide in my game. If the bottom left corner is exposed but the rest are not I would let him say he is scrunched up on the right side of the square ... but in that case he is scrunched up on the right side of the square and he doesn't see the enemy. If lines to all 4 corners are broken he can't see the enemy from that square at all, he needs to move to a different square to get line of sight.
It does not prevent use of the class feature at all. It prevents use of metagaming in a way that was not intended. Being able to hide as a bonus action by itself is huge, with or without the advantage. You can get advantage from it as well, just not in the silly way people here are trying to say you can. You have to shoot from a hidden position, it is that simple.
For example - let's say it one Rogue against 5 orcs. He runs behind a large tree in an otherwise completely open field in broad daylight and takes the hide action. I will agree he is hidden. The Orcs saw him run behind the tree and take ready action and are going to shoot as soon as he sticks his head out. They are staring right at the tree with bows drawn, are you really going to tell me they can't see him when he sticks his head out like the guy in the photo above? If it was your PC playing one of the orcs would you say, "oh yeah he can stick out his head and I won't see him".
Now, how can this Rogue make effective use of his ability? Well instead of sticking his head out he can climb the tree on the backside staying hidden. He could get up on the branches, if there are thick branches and foilage he can sneak out on one of them. He can take the dash action too while hidden and climb/move up to 60' on the tree with climbing counting twice. Now maybe he can make an attack FROM HIDING where he can not be seen by the orcs, being obscured by leaves that do not stop his arrows. Now he can shoot down on one of them. When he does they yell "he is there up in the trees", assuming he didn't dash he can take a bonus action and try to hide again right after the shot, either right where he is or another branch similarly obscured. If successful they don't know where he is in those branches. Is he where he shot from, did he go further down the branch, did he climb back down behind the trunk? The orcs can shoot into the branches, one takes a guess he stayed in the same place and looses an arrow. If he guessed right he rolls with disadvantage. If he guessed wrong it is just a miss. Next turn Rogue does it again .... rinse and repeat.
Now the example I gave above is very difficult situation for the rogue tyring to hide in broad daylight with only one thing to get cover behind. It is not a very favorable setup for the Rogue, but I still gave an example of how he could try to hide AND get advantage. Your Rogue should be looking for these kinds of things to make the most of his abilities, while playing the game RAI.
Another example: You stumble on some orcs in a dungeon. Your Paladin runs forward with the torch in one hand and sword in the other and engages the orcs. You start the turn 25 feet from the orcs. You know they have darkvision and can see in darkness as dim light out to 60 feet. You move 30' backwards and take the dash bonus action to go another 10 feet, putting yourself out of their darkvision range. Now you are in darkness and completely obscured. You can't both hide and attack this turn because you already used your BA. However your enemy can't see you, so you have advantage anyway (you can see them well because they are brightly lit). You shoot with advantage and SA. You are not "hidden" the orcs not fighting the paladin know right where you are and can shoot at you but with disadvantage because they can't "see" you. Next round you shoot again with advantage before hiding, then you take hide, maybe you move to the other side of the hallway or back up another 10 feet, maybe you dont. Now the orcs have to guess where you are to shoot you AND if they guess right they still get disadvantage because they don't see you.
That is how a Rogue should be making effective use of his abilities and getting advantage and SA. Further if the Rogue in the 2nd example had skulker he would not have to retreat 40 feet, he could retreat 20' to get out of the 40 foot torchlight radius and take hide inside the orcs darkvision range because he can hide in dim light. This is not as good in this example because he has to succeed in a hide check, and he can get to actual darkness by taking dash instead but if it was someone with longer darkvision, like Drow it would be an effective way to hide.