While this is true, nail upgrades also trigger a minor health increase for enemies. Speed runners leverage this by skipping nail upgrades and focusing instead on spells, which don't have the same effect- enemy health is balanced around no nail upgrades, so spells are relatively more effective.

Edit: Using the following as a source: https://hollowknight.fandom.com/wiki/Damage_Values_and_Enemy_Health

It looks like many, but not all, enemies receive one or more health boosts in response to nail upgrades. Included in the list of impacted enemies are all the dream warriors, most of the Grim Troupe content, and, weirdly, Husk Sentries (although with their health and positioning in the game it makes sense). All of them appear to still get easier as you upgrade your nail, though it mitigates the degree. I admit I thought it was more extensive than this, so it looks like overall you do benefit from upgrades.