One of the advanced features of SpiderOak is broad deduplication. That means that we try very hard to store new versions of files (and entirely new files and folders) by referencing existing data blocks that were previously stored. (Reference: A 'data block' refers to the way we store you data. We break every file down into very tiny pieces and each of these pieces we call a 'data block'). A data block is deleted (and the space it uses is freed) when there is no longer any reference to that data block.
In general, this means that space usage doesn't always decrease when files are removed - especially if other files are referencing those same data blocks.
As a general example, if you have any two copies of the same file in any combination of folders or on different devices (including deleted files and deleted folders in the Garbage Bin), removing one of them will not free any space -- the space for storing the data is still used by the other copy. In order to completely free up the space you would have to remove both copies of this document.
This also applies to individual data blocks (pieces of files) that are shared across many historical versions of a file. Deleting old versions of a file doesn't free any space if those same data blocks are also used in the newest versions of the file.