You are correct that HP is absent from the damage calculation formula. HP does not change the amount of damage your Pokemon takes (which is the effect of Def and SpD in the formula), but rather changes how much damage your Pokemon can take before it is knocked out.
Imagine you had a Pokemon with 200 HP, which is about to be hit by an attack that will do 100 damage. After the attack, your Pokemon will have 100/200 HP. That means the attack will have done 50% damage to your Pokemon.
Now, imagine you had a Pokemon with 300 HP, and it was hit by the same attack that does 100 damage; it would be left with 200/300 HP. In that case, the attack only took away 33% of its health, even though the damage was the same.
In other words, the 300 HP Pokemon is "more bulky" because it can survive the same attack more times. The Pokemon could also be made bulky if you increased Def or SpD EVs, but that would have the effect of decreasing damage instead (i.e. maybe the attack does 80 damage instead of 100).
Clearly, HP EVs are good because they take you closer to the 33% scenario, instead of the 50% scenario. Also, HP EVs are relevant for both physical and special attacks, while the primary two defensive stats only help with one or the other.
For these reasons, almost all defensive Pokemon use 252 HP before investing anything into the other two stats.
