Ammunition are weapons
If you read closely on the equipment chapter, you will notice that ammunition are weapons just like every other weapon, they simply have different rules governing how they should be used. Here, it says they are used with projectile weapons, so you cannot use ammunition without a projectile weapons (exceptions exists: see throwing arrows).
Every ammunition also has an entry on their weapon table for small and medium creatures separatedly. Those without an entry, use the damage from the ranged weapon or a special rule described on the ammunition's description.
This means that all rules governing weapons (sans exceptions) can be applied to ammunitions aswell, including the rule for Inappropriatedly Sized Weapons:
A weapon’s size category isn’t the same as its size as an object. Instead, a weapon’s size category is keyed to the size of the intended wielder. In general, a light weapon is an object two size categories smaller than the wielder, a one-handed weapon is an object one size category smaller than the wielder, and a two-handed weapon is an object of the same size category as the wielder.
Inappropriately Sized Weapons: A creature can’t make optimum use of a weapon that isn’t properly sized for it. A cumulative –2 penalty applies on attack rolls for each size category of difference between the size of its intended wielder and the size of its actual wielder. If the creature isn’t proficient with the weapon, a –4 nonproficiency penalty also applies.
To give a few examples:
A medium character wielding a medium-sized longbow with small-sized arrows would suffer a -2 penalty on his checks.
A medium character wielding a small-sized longbow with small-sized arrows would suffer only a -4 penalty, as the weapon is innapropriate for his size, and the ammunition being used are innapropriate for his size aswell