First of all, I'm not 100 % sure whether I understand your BoxCryptor + Strato HiDrive configuration, correct me if I made some wrong assumptions.
What I understand so far is :
1) Strato's remote storage is mounted as a WebDAV (SSL) drive.
2) The unencrypted sources that you want to store are somewhere on a local harddisk.
3) Boxcryptor's encryption directory points to a directory that's part of Strato's drive.
4) Rsync is used to synchronize your unencrypted source directory to BoxCryptor's drive, while BC's encrypted directory is part of Strato's drive.
There are several reasons to organize issues a bit differently, because I occasionaly find that Mac OS networking behavior is not what I want.
In addition, rsync clients are meant to talk to rsync servers efficiently, in this case Strato's rsync server, therefore I would use the following configuration:
a) BC's encryption directory is on my local harddisk, most of my home directory files and subdirectories are stored in BC's drive. This has the advantage that in case a laptop is stolen or lost, a desktop or laptop needs to be repaired, most of the data is encrypted.
b) instead of synchronizing an unencrypted directory tree to a BC drive, which encryption directory is part of Strato's storage, synchronize a local encrypted BC directory tree to Strato's rsync server, for example :
rsync -rvt -e "ssh" --progress
The above-mentioned lines are 1 command line, of course.
In case you want to delete backup files or directories that are not part of your local laptop or desktop storage anymore :
rsync -rvt -e "ssh" --progress --delete
This is what I called "connect to Strato's rsync server".
Hope I have not made any typos?
In case you want rsync only to show what it will do, but not apply any changes, add the -n parameter (dry run), etc.
The -e "ssh" implies rsync over ssh, and ssh is quoted because you may add additional ssh args within the quotes.
The first time you connect to Strato's rsync server over SSH, the SSH part of it will prompt you to ask whether to continue, because it's still an unknown machine.
Then it will prompt to enter your Strato HiDrive password.
No need to say you should check the rsync + SSH checkbox in your Strato's admin console (customer login), etc.
I'm not sure whether Strato's free HiDrive account is different from other Strato accounts, but this is how it works for purchased accounts.
Well, just my $0.02