Multimodal Retrieval-Augmented Generation (MRAG) has emerged as a key paradigm for grounding MLLMs with external knowledge. While query pre-processing (e.g., rewriting) is standard in text-based RAG, existing MRAG pipelines predominantly treat visual inputs as static and immutable, implicitly assuming they are noise-free. However, real-world visual queries are often ``imperfect'' -- suffering from geometric distortions, quality degradation, or semantic ambiguity -- leading to catastrophic retrieval failures. To address this gap, we propose V-QPP-Bench, the first comprehensive benchmark dedicated to Visual Query Pre-processing (V-QPP). We formulate V-QPP as an agentic decision-making task where MLLMs must autonomously diagnose imperfections and deploy perceptual tools to refine queries. Our extensive evaluation across 46,700 imperfect queries and diverse MRAG paradigms reveals three critical insights: (1) Vulnerability -- visual imperfections severely degrade both retrieval recall and end-to-end MRAG performance; (2) Restoration Potential \& Bottleneck -- while oracle preprocessing recovers near-perfect performance, off-the-shelf MLLMs struggle with tool selection and parameter prediction without specialized training; and (3) Training Enhancement -- supervised fine-tuning enables compact models to achieve comparable or superior performance to larger proprietary models, demonstrating the benchmark's value for developing robust MRAG systems The code is available at https://github.com/phycholosogy/VQQP_Bench