Ferry quays experience rapid deterioration due to their exposure to harsh maritime environments and operational ferry impacts. Vibration-based structural health monitoring offers a valuable approach to assessing structural integrity and enhancing the understanding of the structural implications of these impacts. However, practical limitations often restrict sensor placement at critical locations. Consequently, virtual sensing techniques become essential for establishing a Digital Twin and estimating the structural response. This study investigates the application of the Gaussian Process Latent Force Model (GPLFM) for virtual sensing through Bayesian inference on the Magerholm ferry quay, combining in-operation experimental data collected during a ferry impact with a detailed physics-based model. The proposed Physics-Encoded Machine Learning model integrates a reduced-order structural model with a data-driven GPLFM representing the unknown impact forces via their modal contributions. This formulation enables joint probabilistic inference of system states and unmeasured responses while accounting for modeling and measurement uncertainties. Results show that the GPLFM provides accurate posterior mean acceleration response estimates at most locations, even under simplifying modeling assumptions such as linear time-invariant behavior during the impact phase. Lower accuracy was observed at locations in the impact zone. A numerical study was conducted to explore an optimal real-world sensor placement strategy using a Backward Sequential Sensor Placement approach. Sensitivity analyses examined the influence of measurement noise, sensor types, incorrectly assumed damping ratios, and sampling frequencies. The results suggest that the GP latent forces can help accommodate modeling and measurement uncertainties, maintaining acceptable estimation accuracy across scenarios.