The forums are mainly for community support and although we regularly swing by, we cannot guarantee any response time here. As a paying customer it would have been better if you used our Helpdesk for your inquiry where we typically reply within 24 hours. You can reach our Helpdesk either via https://www.boxcryptor.com/app/help/user or firstname.lastname@example.org.
Regarding your original question:
We would love to support on-demand downloading of files which are not yet downloaded and only available in iCloud, but Apple simply does not offer this option to third party applications like Boxcryptor. Additionally, iCloud Drive does not have the concept of "downloaded folders" - unlike other storage providers like Dropbox - which will automatically download all new files within a folder. As you mentioned, it is necessary to manually download a file or folder in iCloud Drive so that is locally available on the Mac. Then it can also be accessed in the Boxcryptor Drive.
In summary, iCloud Drive is not very friendly to 3rd party developers and we're doing our best to integrate Boxcryptor as good as possible so that also iCloud Drive users can also encrypt their files. If it still does not work as good as expected, you might want to try Boxcryptor with a different cloud storage provider, e.g. Dropbox.