Moles still work without knowing that atoms exist. The quantity being called "amount of substance" not "number of things" reflects that. However, they are still a redundant over-complicated legacy that doesn't need to exist.

Moles are used because they are useful abstraction. When you want to get from reaction equation to actual real word having some fixed weight is useful. It becomes useful to have fixed relatively usable quantity to work with.

They are relatively decent size for actually weighing out things.

And honestly mapping number of elementary particles directly to grams is not unreasonable. Even if because physics of world are tad weird there is still possibility for some sanity checks.