Hamiltonian neural networks (HNNs) represent a promising class of physics-informed deep learning methods that utilize Hamiltonian theory as foundational knowledge within neural networks. However, their direct application to engineering systems is often challenged by practical issues, including the presence of external inputs, dissipation, and noisy measurements. This paper introduces a novel framework that enhances the capabilities of HNNs to address these real-life factors. We integrate port-Hamiltonian theory into the neural network structure, allowing for the inclusion of external inputs and dissipation, while mitigating the impact of measurement noise through an output-error (OE) model structure. The resulting output error port-Hamiltonian neural networks (OE-pHNNs) can be adapted to tackle modeling complex engineering systems with noisy measurements. Furthermore, we propose the identification of OE-pHNNs based on the subspace encoder approach (SUBNET), which efficiently approximates the complete simulation loss using subsections of the data and uses an encoder function to predict initial states. By integrating SUBNET with OE-pHNNs, we achieve consistent models of complex engineering systems under noisy measurements. In addition, we perform a consistency analysis to ensure the reliability of the proposed data-driven model learning method. We demonstrate the effectiveness of our approach on system identification benchmarks, showing its potential as a powerful tool for modeling dynamic systems in real-world applications.