Basically initially users are scared "wait, why are we deleting something, I didn't delete this much stuff", and then they just stop paying attention to this once they realize this happens all the time.
What's happening, IMU, is that the deleted items are old versions of notes most of the time.
I think there must be a distinction between those in the UI. That is, Joplin should say something along the lines "Deleted old note versions: 12; Deleted noted: 3".
Perhaps this should also apply to "Created" items.
On mobile, a shorter message currently means that more space is available for the notebook list — a long message currently decreases the space available for other items in the sidebar. To address this, it may make sense to either:
Use a status message that isn't long when a large number of different item types have been changed.
Truncate the full status message, if long, and link to a more detailed sync status page.
There is A LOT that happens during the sync process that leaves folks scratching their heads. One thing that is missing is a progress bar for the whole process. Or some indicator stating that 1225/1396 items doesn't mean you a hundred and change items away from completing the sync. For example.