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Quantum Architecture Search (QAS) automates the design of parameterized quantum circuits for variational quantum algorithms, yet existing benchmarks organize instances by molecular identity or qubit count -- criteria agnostic to Hamiltonian structure -- and rely solely on energy accuracy, which cannot detect structural failures such as over-parameterization on near-product ground states. We introduce HamQASBench, a Hamiltonian-informed diagnostic benchmark organizing 11 molecules into five structural tiers via fingerprints derived from the Pauli operator basis, computational basis representation, and ground-state entanglement. A post-hoc critical-structure extraction procedure identifies minimal circuits consistent with each tier's requirements, complementing energy-based evaluation with per-qubit entanglement analysis and pairwise state fidelity. Benchmarking five QAS methods across four paradigms reveals failure modes invisible to conventional metrics: over-parameterization in the minimalism regime, eigenstate commitment under degeneracy, a representation bottleneck in strongly correlated systems, topology-induced routing failure, and circuit search space growth as a scalability bottleneck.