It depends. If you have downloaded BookReader from MacAppStore, your Books repository resides in the sandbox container (~/Library/Containers/com.lymes.BookReader/Data/Books). If you have downloaded the app from this side, you will find your books in ~/Books folder.
It seems inconsiderate to dump the books folder in the root of the home directory. Normally an app would choose its own Application Support folder location, or at least a folder inside the Documents folder.
Is there no option or command that can move the location?
Many users have asked for ~/Books location. Previously I opted for ~/Documents/Books folder, but many users asked to move it to the home directory (perhaps for iCloud sync reasons). Well, there is no “move” books folder feature, but we have a “Choose Books Library Directory” feature in our ToDo list. Stay tuned!