In recent years, research in the space community has shown a growing interest in Artificial Intelligence (AI), mostly driven by systems miniaturization and commercial competition. In particular, the application of Deep Learning (DL) techniques on board Earth Observation (EO) satellites might lead to numerous advantages in terms of mitigation of downlink bandwidth constraints, costs, and increment of the satellite autonomy. In this framework, the CloudScout project, funded by the European Space Agency (ESA), represents the first time in-orbit demonstration of a Convolutional Neural Network (CNN) applied to hyperspectral images for cloud detection. The first instance of this use case has been done with an INTEL Myriad 2 VPU on board a CubeSat optimized for low cost, size, and power efficiency. Nevertheless, this solution introduces multiple drawbacks due to its design not specifically being for the space environment, thus limiting its applicability to short-lifetime Low Earth Orbit (LEO) applications. The current work provides a benchmark between the Myriad 2 and our custom hardware accelerator designed for Field Programmable Gate Arrays (FPGAs). The metrics used for comparison include inference time, power consumption, space qualification, and components. The obtained results show that the FPGA-based solution is characterized by a reduced inference time, and a higher possibility of customization, but at the cost of greater power consumption and a longer Time to Market. As a conclusion, the proposed approach might extend the potential market of DL-based solutions to long-term LEO or interplanetary exploration missions through deployment on space-qualified FPGAs, with a limited cost in energy efficiency.