The evaluation of Deep Research Agents is a critical challenge, as conventional outcome-based metrics fail to capture the nuances of their complex reasoning. Current evaluation faces two primary challenges: 1) a reliance on singular metrics like Pass@1, creating a "high-score illusion" that ignores the quality, efficiency, and soundness of the reasoning process; and 2) the failure of static benchmarks to quantify crucial attributes like robustness and latent capability. To address these gaps, we introduce TRACE (Trajectory-Aware Comprehensive Evaluation), a framework that holistically assesses the entire problem-solving trajectory. To counter the "high-score illusion", we propose a Hierarchical Trajectory Utility Function that quantifies process efficiency and cognitive quality, including evidence grounding, alongside accuracy. To measure deeper attributes, TRACE introduces a Scaffolded Capability Assessment protocol, quantifying an agent's latent ability by determining the minimum guidance needed for success. Our contributions include the TRACE framework, its novel metrics, and the accompanying DeepResearch-Bench with controllable complexity. Experiments show TRACE delivers a granular ranking that uncovers critical trade-offs between agent accuracy, efficiency, and robustness entirely missed by singular metrics.