In this paper, we study short-packet communications in multi-hop networks with wireless energy transfer, where relay nodes harvest energy from power beacons to transmit short packets to multiple destinations. It is proposed a novel cooperative beamforming relay selection (CRS) scheme which incorporates partial relay selection and distributed multiuser beamforming to achieve a high-reliable transmission in two consecutive hops. A closed-form expression for the average block error rate (BLER) of the CRS scheme is derived, based on which an asymptotic analysis is also carried out. To achieve optimal channel uses allocation, we formulate a fairness end-toend throughput maximization problem which is generally NPhard due to the non-concavity of the objective function and mixed-integer constraints. To solve this challenging problem efficiently, we first relax channel uses to be continuous and transform the relaxed problem into an equivalent non-convex one, but with a more tractable form. We then develop a lowcomplexity iterative algorithm relying on inner approximation framework to convexify non-convex parts that converges to at least a locally optimal solution. Towards real-time settings, we design an efficient deep convolutional neural network (CNN) with multiscale-accumulation connections to achieve the suboptimal solution of the relaxed problem via real-time inference processes. Numerical results are presented to verify the analytical derivations and to demonstrate performance improvements of the CRS scheme over the benchmark ones in terms of BLER, reliability, latency, and throughput in various settings. Moreover, the designed CNN provides the lowest root-mean-square error compared to the state-of-the-art deep learning approaches while the CNN-aided optimization framework estimates accurately the optimal channel uses allocation with low execution time.