It was observed that the document count for the Notes mail file showed X and NME showed that it had found Y documents to migrate.
This caused by where and when the information is gathered. The information listed on the Notes database contains All document in the Mail file, including deleted items, corrupt documents and profile documents.
The reason you see a difference in the document count is down to the quality of the information and the time elapsed since updates were last run.
The data is only going to be accurate as the last time the "Locate Notes Datastore" is run and if NME was able to read the data. All these numbers are estimates. NME does not get the actual numbers since it would have to open each NSF and manually count the messages. NSF database is usually larger than the amount of data in it since it is a database and holds everything; deleted items are not removed until the database is compacted. Scanning catalog.nsf is the best NME can do and that information is typically out of date depending on what that server task last ran.
If it is imperative that that document count is matching, or close to the same, then:
The document numbers will never be exactly the same but will be close to each other.