I recently archived a large project after processing. It contained 18TB and 1.6 million files. When I discussed this with our sysadmins they were shocked by the number of files and links. Just the file list is >200MB, so file listing and tar operations are very slow. This caused some real issues with our archive system performance. This is perhaps an extreme case, but in my experience projects with hundreds of thousands of files are pretty common.
I wonder if CryoSparc should consider using techniques to reduce the number of files, such as storing images in HDF5 files. This is common in other fields, eg serial crystallography where they have extremely large numbers of images.