I have been trying to get Boxcryptor to play nice with Spotlight but it has been a no go.
There is a way to turn it on. However, it has not worked for me.
I have found a work around with using the out-of-beta version 1 of Quicksilver. By putting the Boxcryptor volume into the Quicksilver catalog, I get an index of the Boxcryptor volume.
It is not a perfect solution. Searching for a folder when saving still requires Spotlight (which still won’t work even if you have Quicksilver installed). However, this work around does the job if you are just looking for files on your hard drive.