every theorem is only as powerful as its assumptions (and propositions). The answers are clearly that
- The LSZ formula always works for the field theories where it's used.
- No actual calculation relevant to physics fails because of Haag's theorem. Haag's theorem is just a philosophy.
Haag's theorem is morally wrong because it studies the question whether the operators in the interacting theory are "strictly" unitarily equivalent to those in the free theory:
$$O_\mathrm{interacting} = U O_\mathrm{free} U^{-1}$$
Not surprisingly, Haag finds out that such a unitary equivalence doesn't exist. This is not surprising because, as we know, operators acquire anomalous dimensions from the interactions (and quantum effects), among other deviations from the classical intuition, and the naive algebra that is valid in the free theory simply no longer applies to the interacting theory.
In particular, the addition of the interactions also modifies the commutation relations between the fields that "directly" create and annihilate the particles - at least the low-energy effective fields. For example, the quantum effects produce effective Lagrangians that contain higher-derivative terms, including new terms with time-derivatives, and the latter modify the canonical momenta and/or the canonical commutation relations. When one is rigorous, many things change when the interactions are added. Haag only assumed that "some" things change, so his results are inconsequential for physics.
At any rate, this 1955 theorem is obsolete - much like most of the former discipline that used to be known as algebraic quantum field theory or axiomatic field theory - and be sure that interacting quantum field theories exist - lattice QCD is an example of a specific way how to define them - and it is equally true that the perturbative approximation of all the physical amplitudes may be calculated by the usual perturbative methods, with the extra philosophy and rigorous refinements given e.g. by the LSZ formalism you mentioned.
Haag's theorem was invented as an attempt to show that there was something wrong with one of the first loop diagrams people understood - the vacuum polarization graph. Mr Haag didn't like them. However, there is nothing wrong with the loop diagram - or any other loop diagrams that became the bulk of knowledge about particle physics in the subsequent decades. The developments in renormalization showed that the calculations, including the loops, are totally valid. The renormalization group made some further progress - it explained why the theories are universal and why the subtraction of infinities work. Haag's theorem became misleading and obsolete in the 1970s.
In particular, the LSZ formalism uses the "adiabatic hypothesis", the assumption that one may neglect the interactions between the particles in the asymptotically distant past. By slowly and continuously turning on the coupling constant, we may map the states of free particles to the states describing particles in the interacting Hilbert space. This is possible as long as all distances between the particles are large. However, this procedure wouldn't work for general configurations of nearby particles - so one can't promote this trick into a full-fledged "canonical" unitary equivalence between the free and interacting Hilbert spaces. There is clearly no such a "natural" or "unique" or "canonical" isomorphism because the free and interacting theories are physically inequivalent. When understood rationally, Haag's theorem is not saying anything else than this self-evident proposition. However, such an isomorphism is not needed to calculate physically meaningful quantities such as the scattering amplitudes.
At least from the viewpoint of physics as an empirical science, it should be clear that the actual calculations in QFT are good science - one that has made predictions and has passed tests comparing the predictions with experiments - while Haag's theorem is not because it hasn't predicted anything that has passed empirical tests. Haag's theorem tries to find problems with the fact that quantum field theory contains new effects such as renormalization that don't appear in quantum mechanics with a finite number of degrees of freedom. However, these extra effects of quantum field theory are real and essential and they lead to no inconsistencies.
Haag's theorem is not a tool to do particle physics; it's an excuse for someone who doesn't want to study particle physics. As every theorem, it says "A implies B". Because we know that B is incorrect - perturbative QFT clearly works - it follows that the assumptions A aren't right.