Could you share some details about how data stored on WP Commander systems is protected? Is the data encrypted? If yes, is each client's data encrypted with unique keys?

All the site data is encrypted using standard encryption(with encryption it is best to follow standards and not invent something new) algorithms and strong keys. Each key is unique for a site, giving even lower level granularity (in comparison to client specific key). The key is stored independently from the actual backup data. This ensures further security of the data.