The culprit is Spotlight rather than Boxcryptor. Boxcryptor only requires CPU time if another process is accessing the Boxcryptor drive - if there's no activity in the Boxcryptor drive, Boxcryptor will not consume any noticeable CPU resources.
If you enable Spotlight for the Boxcryptor drive, Spotlight has to index all files in the Boxcryptor drive. During this indexing process, Spotlight must read all files in the Boxcryptor drive. This causes a huge amount of file and decryption operations which in turn lead to the observed CPU load.
The good thing is, that the initial indexing is a one time process - once indexing has finished, only newly added files have to be scanned and CPU load due to Spotlight should not be an issue anymore. If you need Spotlight, I'd recommend to enable it e.g. in the evening and leave your MacBook powered on during the night (and connected to a power outlet) so that Spotlight can perform the initial indexing.