I cannot claim to be an expert on AQFT, but the parts that I'm familiar with rely on local fields quite a bit.
First, a clarification. In your question, I think you may be conflating two ideas: local fields ($\phi(x)$, $F^{\mu\nu}(x)$, $\bar{\psi}\psi(x)$, etc) and unobservable local fields ($A_\mu(x)$, $g_{\mu\nu}(x)$, $\psi(x)$, etc).
Local fields are certainly recognizable in AQFT, even if they are not used everywhere. In the Haag-Kastler or Brunetti-Fredenhagen-Verch (aka Locally Covariant Quantum Field Theory or LQFT), you can think of algebras assigned to spacetime regions by a functor, $U\mapsto \mathcal{A}(U)$. These could be causal diamonds in Minkowski space (Haag-Kastler) or globally hyperbolic spacetimes (LCQFT). You can also have a functor assigning smooth compactly supported test functions to spacetime regions, $U\mapsto \mathcal{D}(U)$. A local field is then a natural transformation $\Phi\colon \mathcal{D} \to \mathcal{A}$ between these two functors. Unwrapping the definition of a natural transformation, you find for every spacetime region $U$ a map $\Phi_U\colon \mathcal{D}(U)\to \mathcal{A}(U)$, such that $\Phi_U(f)$ behaves morally as a smeared field, $\int \mathrm{d}x\, f(x) \Phi(x)$ in physics notation.
This notion of smeared field is certainly in use in the algebraic constructions of free fields as well as in the perturbative renormalization of interacting LCQFTs (as developed in the last decade and a half by Hollands, Wald, Brunetti, Fredenhagen, Verch, etc), where locality is certainly taken very seriously.
Now, my understanding of unobservable local fields is unfortunately much murkier. But I believe that they are indeed absent from the algebras of observables that one would ideally work with. For instance, following the Haag-Kastler axioms, localized algebras of observables must commute when spacelike separated. That is impossible if you consider smeared fermionic fields as elements of your algebra. However, I think at least the fermionic fields can be recovered via the DHR analysis of superselection sectors. The issue with unobservable fields with local gauge symmetries is much less clear (at least to me) and may not be completely settled yet (though see some speculative comments on my part here).
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