Classical spectral descriptors such as the Heat Kernel Signature and Wave Kernel Signature are widely used for non-rigid 3D shape retrieval, yet their failure modes remain poorly understood. We present a frequency-scale saliency framework that audits these descriptors by quantifying the retrieval-level contribution of each descriptor scale interval through ablation. We introduce class spectral fingerprints to characterize category-level scale dependence, and show that descriptor similarity between class pairs is substantially correlated with retrieval failure, with a Spearman correlation of 0.479. Experiments on SHREC'11 demonstrate that short scales dominate retrieval performance while long scales are harmful, that HKS and WKS exhibit distinct scale dependence patterns, and that saliency-weighted retrieval improves mAP on hard categories by 0.156, with cross-fold and random-weight controls confirming that the gain is stable and not due to arbitrary reweighting.