I don't know that you're going to get a fantastic answer on this. The concept behind compacting the databases to identify and compress those items that have compression attributes not all forms of data can be compressed... Tape drives work on the same native basis- tape drives can only compact information that have attributes that allow it to be compacted...
An example of this would be a JPEG image; JPEG images already have a compression ratio applied to them in most cases. So copying and pasting a JPEG image into MyNotesKeeper and then later coming back to compact the file, you're not going to get the great compression ratio.
And in regards to the file, your file, going from 70+ megabytes to 50+ megabytes is a pretty good ratio. I don't know why you'd be unpleasantly surprised; I would say was doing pretty good.
MyNotesKeeper files can be pretty big, and compacting those large files can take some processing time, and resources [...] and thus far the maintenance of the database has been a manual process, but it's not completely out of the scope of logic. \

A suggestion could be made to allow MyNotesKeeper to do maintenance on the database if the system is idle, but then you run the risk of a user trying to use their system while MyNotesKeeper is trying to optimize the file, and then dealing with the complaints of MyNotesKeeper interfering with their system performance. It's a double-edged sword...
I hope this helps...
Thanks,
Stingray57
MyNotesKeeper v1.9.9
Microsoft Vista HP x64/ XP / 7 and Ubuntu