The performance of Boxcryptor Classic can vary depending on number of files in a Boxcryptor Classic Folder if you have filename encryption enabled. When a program tries to access a file in the BC Classic drive with different upper and lower case characters then the file actually has (e.g. FILE.TXT instead of file.txt), then Boxcryptor has to fetch the whole folder content and decrypt every filename to compare the plaintext filename with the requested filename. If the folder structure is very nested with lots of file on every level, this can slow down the performance - especially when the BC Classic folder is located on a remote storage (e.g. NAS).
Another consideration might be security. All files in a BC Classic folder are encrypted with the same encryption key and protected by the same password. Splitting a BC Classic folder into multiple folders might increase the security in case one password gets leaked.
Personally, I'd break down the BC Classic folders on access (one folder for a specific group, organizational unit, project, etc.) - the size itself should not have a too big impact.