In Domino 8.0.2 and later, IBM decided to no longer calculate the "Application percent used" by default in the catalog.nsf file. Here is a link to an IBM article: CATALOG_DISK_USAGE. Setting "CATALOG_DISK_USAGE=1" in the notes.ini on the Domino servers hosting user mail files should populate the "Application percent used" field in the catalog.nsf, allowing MNE to gather accurate mail file sizes.
Note: As described in the IBM article, setting "CATALOG_DISK_USAGE=1" may cause additional resource usage on the Domino server. We would suggest reaching out to IBM directly for any additional details about the "CATALOG_DISK_USAGE" setting.