[RPG] Do crossbows and other noted exceptions miss past their long range underwater

About ranged attacks

Ranged weapons have a normal range and a long range. Under normal circumstances, you can attack enemies which are within your long range, but as soon as they are beyond normal range you have disadvantage on the attack. Attacking a creature while engaged in close combat does also impose disadvantage on ranged attacks. (PHB p.195)

Underwater Combat

In the special case of underwater combat, an attack beyond normal range is an automatic miss and an attack within normal range is at disadvantage unless it is one of the explicitly stated. This rule is a specific beats general case regarding ranged attacks and their two ranges.

[...] against a target within normal range, the attack roll has disadvantage unless the weapon is a crossbow, a net, or a weapon that is thrown like a javelin (including a spear, trident, or dart)

This means, that nets are excluded from the water's specific case rule regarding attacks within normal range. So the long range is a automatic miss rule still applies to them.

The disadvantage for attacks with a net is not caused by its range, but by close combat

The rules of ranged attacks in close combat do still apply. You could still use e.g. a crossbow under water to attack a creature 10ft away from you without getting disadvantage due to the range category, but when you are engaged in close combat you still get disadvantage on ranged attacks (unless you got the crossbow expert feat) same applies for nets.

No, you don't add those

The section of the rules on damage rolls states (PHB, p. 195):

When attacking with a weapon, you add your ability modifier—the same modifier used for the attack roll — to the damage. A spell tells you which dice to roll for damage and whether to add any modifiers.

While you are making a ranged weapon attack, the damage is that specified in the spell (4d8 lightning) "instead of the weapon’s normal damage." The weapon's normal damage may include your Dex (or Str) modifier and may include sharpshooter but the spell damage doesn't.