In this case, you have completely changed the rules for underwater combat, which say that ranged weapons miss at long range and apply disadvantage at short range.
Now that might be fine, but it's something you should probably have advised players about up front, not suddenly sprung on them once an encounter has already started. Or worse, once they've expended resources to get a clear shot at the dragon that you decide to disallow.
In that case, part of the issue is that you're mixing up concealment and cover. The rules cover it fine. You, as the DM, can say "you can't see the creature", or you can set a DC to spot it. You don't go "it gets 3/4 cover because it's hard to see". After all, being completely invisible only grants disadvantage.
At some point, rules can't be too awful and far from reality, or the game just sucks. "Water is an impenetrable wall... when my monster wants to use it to ambush from" is one of those points.
Sure they do, it's an effect that is negated with practise when fishing, and it doesn't matter a whole lot when you are talking about perpendicular angles and monster sized targets. Call it out in the narrative of failed attack rolls, and you are done.The rules also don't account for diffraction and so forth.
I wouldn't bother. The dragon will already be wholly in the darkness between it's turns, and readying is already going to be frustrating enough without adding arbitrary penalties to the resultant attack rolls. There's also some question as to just why it is more difficult to hit a head that is the size of a man when you can't see the dragon body, which is kind of like it becoming more difficult to hit a man on a horse when you can't see his horse...But a related question: how would you adjust attacking a dragon who's head is sticking out of a sphere of darkness? Would it be more difficult to hit than if you could see the whole dragon?
I wouldn't bother. The dragon will already be wholly in the darkness between it's turns, and readying is already going to be frustrating enough without adding arbitrary penalties to the resultant attack rolls. There's also some question as to just why it is more difficult to hit a head that is the size of a man when you can't see the dragon body, which is kind of like it becoming more difficult to hit a man on a horse when you can't see his horse...
Observation of a few baseline creatures (elk vs giant elk, bat vs giant bat, horse vs rhino vs elephant, pseudodragon vs various dragon sizes) doesn't suggest there's any inverse relationship between size and AC. They all have some modicum of natural armor plus their dex mod.Right ... but assume for the moment a huge dragon in a large globe of darkness. Pieces (but not the whole dragon) are sticking out.
As far as hitting just the head, the AC of a dragon normally takes into account you can target the entire dragon.
Anyway, rule it any way you want. I just don't think the rules are quite as clear cut as you do.
You're the one saying "this is a good general rule for cover from water or concealment from darkness, regardless of circumstance". I'm saying "this is a ruling specific to the situation, and for most situations a DM should make up something else, because this rule is particularly harsh".
In my limited experience, spear/bow fishing is getting fish within the first few feet of water, probably no more than 5 ft or so. According to a quick google search, the maximum a modern spearfishing gun could be effective is 30 ft, and even that is pushing it. Assuming you don't have a whaling harpoon handy, attacking submerged creatures should not be simple.
So I would say that anything under 10-15 ft of water is probably not going to be hit by most ranged weapons.
Part of the issue is that the rules don't really deal well with terminology around partially concealed creatures. If you're facing a black dragon in a dark lake, you're not going to be able to see most of the dragon, but the rules don't really cover that.
In any case, I'd just use the ruling from the adventure. At a certain point, D&D can't be too realistic or it starts becoming too difficult to play.