Yes, it applies to all (normal) projectiles fired through the wall
As you noted, the wind wall spell creates a wall of wind that blows upward, and says:
Small or smaller flying creatures or objects can't pass through the wall. Loose, lightweight materials brought into the wall fly upward. Arrows, bolts, and other ordinary projectiles launched at targets behind the wall are deflected upward and automatically miss. (Boulders hurled by giants or siege engines, and similar projectiles, are unaffected.)
This is true of creatures and objects that meet this description, regardless of whether they are associated with the caster, their allies, or their enemies.
All physical thrown weapons or ammunition/projectiles for ranged weapons would probably be considered "Small or smaller [...] objects", which can't pass through the wall. (Ranged spells, in contrast, are not "ordinary projectiles", and aren't objects either, so they would probably be able to pass through the wall.)
Spells do what they say they do; if there's no exception for or specification of which creatures or objects the spell's effects apply to, it applies to all creatures or objects per the description.