If part of the target is visible above the wall, the existing rules for half or three-quarters cover address the situation adequately, without having to complicate the matter by deciding whether the archers would be using direct or indirect fire. You can assume that the archers are using whatever form of fire is most effective for the situation and that RAW (those adjusting for cover) apply.
However, it may be the case that the archers wish to fire on targets which are behind a wall which is higher than the targets. That is, there may be targets which, in two dimensions, are behind complete cover and thus are not targetable RAW, but for whom indirect fire is a realistic option.
If you wish to permit indirect fire as a non-RAW option...
You can use siege weapons as a model
While combat in three dimensions is largely unsupported in 5e, and archers using indirect fire is not explicitly mentioned, there are two siege weapons that explicitly use indirect fire. Rules that already exist can guide you if you as a DM decide to make this a homebrew option.
From Siege Equipment, DMG 255-256 (emphases mine)
A mangonel is a type of catapult that hurls heavy projectiles in a high arc. This payload can hit targets behind cover. Before the mangonel can be fired, it must be loaded and aimed. It takes two actions to load the weapon, two actions to aim it, and one action to fire it. A mangonel typically hurls a heavy stone, although it can hurl other kinds of projectiles, with different effects.
Mangonel Stone. Ranged Weapon Attack: +5 to hit, range 200/800 ft. (can't hit targets within 60 feet of it), one target. Hit: 27 (5d10) bludgeoning damage.
A trebuchet is a powerful catapult that throws its payload in a high arc, so it can hit targets behind cover. Before the trebuchet can be fired , it must be loaded and aimed. It takes two actions to load the weapon, two actions to aim it, and one action to fire it. A trebuchet typically hurls a heavy stone. However, it can launch other kinds of projectiles, such as barrels of oil or sewage, with different effects.
Trebuchet Stone. Ranged Weapon Attack: +5 to hit, range 300/1,200 ft. (can't hit targets within 60 feet of it) one target. Hit: 44 (8d10) bludgeoning damage.
From these descriptions it is clear that indirect fire is a 'thing' in 5e. Since the ballista (DMG 255) is a direct-fire siege weapon, we can compare its features to those of a mangonel and trebuchet to see what effects, RAW, indirect fire imposes. That can then give us a baseline for how to modify archer fire while remaining within the spirit of RAW.
First, note that while both of the indirect-fire weapons are at +5 to hit, the ballista is at +6 (and the ram at +8). It seems reasonable that it is harder to hit a target with indirect fire. Archers firing indirectly should be assigned a penalty to hit.
Second, both of the indirect fire weapons have minimum ranges of 60 feet, while the ballista does not have a minimum range. Presumably this is in part because of the technological limitations of the weapon, but also because the high arc required to hit such a close target would make the resultant shot so inaccurate as to not be worth it (and would possibly include the weapon itself in the area potentially receiving fire). You could get pedantic with arcs and describing projectile motion, but the siege weapon descriptions have a minimum range of 1/3rd to 1/5th normal range. A similar minimum for the archers would be appropriate.
Third, "Siege weapons are designed to assail castles and other walled fortifications." (DMG 255) Implicit in this is that they are operating outside - with no ceiling that could intercept a high arc. Again, you can calculate firing arcs, or you can adopt a simplistic rule such as that when indoors, or underground, your archers can't fire on anything further from them than twice the height of the ceiling.
Fourth, as siege weapons, their targets are typically buildings, defensive fortifications, and other siege weapons, none of which move during the time frame of their firing. Since their target isn't moving, it is not as important whether they can see the target or not on an ongoing basis. If the targets of the archers are both behind total cover and moving, I would suggest using the standard penalty of disadvantage on attacks for opponents you cannot see.
Finally, because of the angle of the descending arc, indirect fire won't be able to easily hit thin creatures that are deliberately snug up against the far side of a wall. It is still appropriate to give targets an AC bonus due to cover if they are using this to their advantage.