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Background and Objectives: The variability and biases in the real-world performance benchmarking of deep learning models for medical imaging compromise their trustworthiness for real-world deployment. The common approach of holding out a single fixed test set fails to quantify the variance in the estimation of test performance metrics. This study introduces NACHOS (Nested and Automated Cross-validation and Hyperparameter Optimization using Supercomputing) to reduce and quantify the variance of test performance metrics of deep learning models. Methods: NACHOS integrates Nested Cross-Validation (NCV) and Automated Hyperparameter Optimization (AHPO) within a parallelized high-performance computing (HPC) framework. NACHOS was demonstrated on a chest X-ray repository and an Optical Coherence Tomography (OCT) dataset under multiple data partitioning schemes. Beyond performance estimation, DACHOS (Deployment with Automated Cross-validation and Hyperparameter Optimization using Supercomputing) is introduced to leverage AHPO and cross-validation to build the final model on the full dataset, improving expected deployment performance. Results: The findings underscore the importance of NCV in quantifying and reducing estimation variance, AHPO in optimizing hyperparameters consistently across test folds, and HPC in ensuring computational feasibility. Conclusions: By integrating these methodologies, NACHOS and DACHOS provide a scalable, reproducible, and trustworthy framework for DL model evaluation and deployment in medical imaging. To maximize public availability, the full open-source codebase is provided at https://github.com/thepanlab/NACHOS.