In cases such as yours, I’d rather sync outside of cryptomator, if you don’t want to have all content backed/synced, try to arrange the vaults so that it could be done since the structure needs to be intact.
as you are actually using Cyberduck, I assumed that you do not want to have you encrypted vault files local on your computer.
If I am right, I actually see no other way than using Cyberduck or Mountain Duck to achieve an automated sync without having the encrypted vault files local.
If I am wrong, and you do not care if the encrypted vault files are also local, then just use any sync software that you like to sync all the encrypted files of your vault (the folder where the “d” and “m” subfolders and the masterkey files are stored) with whatever destination you want to.
Here I describe how I do my backups automatically (personal backup as backup tool of unencrypted files into the vault, OneDrive client as sync tool to sync the encrypted files to OneDrive4Business).