You are correct that HP is absent from the damage calculation formula. HP does not change the amount of damage your Pokemon receives (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 be left with 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 33.3% of its health, even though the damage was the same. 100 damage was a lower amount relative to the total your Pokemon could take.
In other words, the Pokemon with 300 HP could take the 100 HP attack three times, while the 200 HP Pokemon could only take it twice. In that sense, the 300 HP Pokemon is "more bulky". It could also be made more bulky if you increase 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).
So, to link back to EVs in competitive, giving HP EVs limits the proportion of your Pokemon's health that is taken away when it is hit by an attack. HP is even more prevalent because it helps with both physical and special attacks, making it the most efficient investment for the vast majority of Pokemon.