It's not really about the encryption directly; it's about the way the database design has to change to support zero knowledge (the server can no longer do the database work.) Things like garbage collection have to happen client side. Described in detail here: https://spideroak.com/blog/20091026143000-why-and-how-spider...
FYI, when SpiderOak first starts running, like any backup software, it has to scan your filesystem to see what may have changed while it was shutdown, and that can take a lot of IO and CPU if you have many folders and/or many small files (hundreds of thousands). (SpiderOak works with any folders you like, including externa/network drives, not just one folder like Dropbox.)
In a profile, basically none of this CPU time is spent in the crypto module, just mostly for unserializing the per-folder journal to compare state. SpiderOak does some optimizations with directory hashing to avoid having to open the journal to scan for specific changes in unchanged folders, but there are some situations where that optimization is defeated (such as if you remount a file system with changed gids, inode IDs, timestamps, etc.)
Anyway, once it's running, it uses the operating system facilities on Linux/Mac/Windows to notice changes automatically so rescanning the whole backup selection after startup is not usually necessary.
In any case, thanks for your interest in SpiderOak. :)