Thanks for your feedback. The main reason for a slower copy process of many small files in contrast to a few large files is that such a copy process requires A LOT more file operations. When copying a large file, a typical write operation has 65 KB or even more. Copying 65 KB of small 5 KB files on the other hand requires 13 write operations - in contrast to 1. Additionally, the copy process does involve a lot more file operations for a single file then just write (e.g. checking of the file exists, checking if it was written, etc.) - with each of them required encryption/decryption of filenames. I hope this explains a little bit why the performance is x-times worse for many small files than larger files.
The current performance of BoxCryptor should be sufficient for most use cases - but of course we're always working on improving it.