You are right: $X_{ét}$ is large (in fact, essentially large). This means that there is no category of presheaves on $X_{ét}$ in ZFC, or if you are using universes you would need to go to a higher universe to talk about the category of presheaves.
However, the category of _sheaves_ $Sh(X_{ét})$ is indeed a genuine category that can be defined without enlarging your universe. This is because there is a small set of objects of $X_{ét}$ which can be used to cover all other objects, and so a sheaf is uniquely determined by the values it takes on a small subcategory of $X_{ét}$. Indeed, since an étale map is locally of finite presentation, it suffices to consider affine schemes which are finitely presented étale covers of affine open subsets of $X$, and there is an (essentially) small set of these.