The Skeletal Archer Template does not increase the skeletons effective Hit Dice for the purposes of Animate Dead, nor should it.
Only templates that specifically say so will increase a creatures effective Hit Dice for the purposes of Animate Dead, that is to say, only Bloody and Burning Skeletons count as additional hit dice when determining how many undead you can create and control with the spell, and for good reason.
Burning and Bloody skeletons are significantly more powerful than a typical skeleton. Burning skeletons have a 2 point higher Charisma score, deal a bonus d6 of fire damage on all melee attacks, and have the Fiery Aura, which deals damage to everyone nearby with no save, and Fiery Death special abilities, meaning they deal a rather high amount of damage for the creatures CR.
Bloody Skeletons have the advantage of being nearly unkillable unless you use a specific means of killing it, plus Fast Healing, channel resistance, and a 4 point higher Charisma score.
The Skeletal Archer, meanwhile, gets the bare minimum of archery feats needed to even function as an archer, and that’s it.