If part of the target is in view 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 they are using whatever is appropriate for the situation and that RAW apply.
However, it may be the case that the archers wish to fire on targets which are behind a wall 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 that as an option beyond RAW...
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 (emphasis 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. Comparing these siege weapons to a direct-fire siege weapon (the ballista, DMG 255) will give us a basis for modifying the attacks of your archers.
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 to assign a penalty to hit for an archer's indirect fire, or perhaps a reduction in the amount of proficiency bonus that can be used.
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 because the high arc required to hit a target any closer than that 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 projectile motion, or you could borrow from the two siege weapon descriptions and assign a minimum value as around 1/3rd to 1/5th short range.
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 to intercept a firing arc. Again, you can calculate firing arcs, or you can adopt a simplistic rule 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 typically are buildings, defensive fortifications, and other siege weapons, none of which move during the time frame of firing. Since their target isn't moving, it is not as important whether they can see the target or not. For archers attempting indirect fire at targets behind cover, I would suggest using the standard penalty of disadvantage on attacks for opponents you cannot see.
Finally, realize that 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.