When the files are encrypted, you cannot use Spotlight to search the files in Dropbox anymore (because Spotlight cannot read them). The solution would be to enable Spotlight on the virtual Boxcryptor Disk (where files are available in plaintext). As you noted, this option is currently not available as we're still working on it. Due to its complexity I cannot give you an ETA yet, when it will be available. Sorry.
Regarding the memory usage: We noticed that version 2.0.401 had a memory leak which caused Boxcryptor to use so much RAM. Just before christmas, we have released version 2.0.403 where this memory leak has been fixed and memory usage should be much lower. You can download it here:
I'm sorry that your experience was not the best. We're doing our best to further improve Boxcryptor for Mac OS X as soon as possible.